0.017167
0.000000
0.000000
0.000000
0.011635
0.000000
0.000000
0.000000
0.021492
0.000000
0.000000
0.000000
Adachi, M.
Hidaka, K.
Kuroki, R.
Kiso, Y.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
58.250
85.948
46.529
C41 H48 N4 O8 S
756.907
(4R)-N-[(2,6-dimethylphenyl)methyl]-3-[(2S,3S)-3-[[(2S)-2-[(7-methoxy-1-benzofuran-2-yl)carbonylamino]-2-[(3R)-oxolan-3 -yl]ethanoyl]amino]-2-oxidanyl-4-phenyl-butanoyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide
KNI-1657
peptide-like
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C3 H8 O3
92.094
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
non-polymer
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
Y
1
N
C
Y
2
N
C
Y
3
N
C
Y
4
N
C
Y
5
N
C
Y
6
N
C
N
7
N
C
Y
8
N
C
Y
9
N
C
N
10
N
C
N
11
N
O
N
12
N
O
Y
13
N
O
N
14
S
C
N
15
N
N
N
16
R
C
N
17
N
C
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
O
N
22
N
O
N
23
N
C
N
24
N
N
N
25
N
O
N
26
S
C
Y
27
N
C
N
28
N
C
Y
29
N
C
N
30
S
C
N
31
N
O
Y
32
N
C
Y
33
N
C
Y
34
N
C
Y
35
N
C
N
36
N
C
N
37
N
N
N
38
N
O
N
39
R
C
N
40
N
C
N
41
N
C
N
42
N
C
N
43
N
C
N
44
N
S
N
45
N
C
N
46
N
N
N
47
N
C
Y
48
N
C
Y
49
N
C
Y
50
N
C
Y
51
N
C
Y
52
N
C
N
53
N
C
Y
54
N
C
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
N
N
104
S
C
N
105
N
C
N
106
N
O
N
107
N
C
N
108
N
O
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
N
N
117
S
C
N
118
N
C
N
119
N
O
N
120
N
C
N
121
N
C
N
122
N
C
N
123
N
N
N
124
N
C
N
125
N
N
N
126
N
N
N
127
N
O
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
N
N
144
S
C
N
145
N
C
N
146
N
O
N
147
N
C
N
148
N
C
N
149
N
O
N
150
N
N
N
151
N
O
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
N
N
161
S
C
N
162
N
C
N
163
N
O
N
164
N
C
N
165
N
C
N
166
N
O
N
167
N
O
N
168
N
O
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
N
N
177
S
C
N
178
N
C
N
179
N
O
N
180
N
C
N
181
N
C
N
182
N
C
N
183
N
O
N
184
N
N
N
185
N
O
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
N
N
197
S
C
N
198
N
C
N
199
N
O
N
200
N
C
N
201
N
C
N
202
N
C
N
203
N
O
N
204
N
O
N
205
N
O
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
N
N
216
N
C
N
217
N
C
N
218
N
O
N
219
N
O
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
C
N
226
N
O
N
227
N
C
N
228
N
O
N
229
N
C
N
230
N
O
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
N
N
240
S
C
N
241
N
C
N
242
N
O
N
243
N
C
Y
244
N
C
Y
245
N
N
Y
246
N
C
Y
247
N
C
Y
248
N
N
N
249
N
O
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
O
N
261
N
H
N
262
N
H
N
263
N
N
N
264
S
C
N
265
N
C
N
266
N
O
N
267
S
C
N
268
N
C
N
269
N
C
N
270
N
C
N
271
N
O
N
272
N
H
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
N
N
286
S
C
N
287
N
C
N
288
N
O
N
289
N
C
N
290
N
C
N
291
N
C
N
292
N
C
N
293
N
O
N
294
N
H
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
N
N
308
S
C
N
309
N
C
N
310
N
O
N
311
N
C
N
312
N
C
N
313
N
C
N
314
N
C
N
315
N
N
N
316
N
O
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
H
N
332
N
N
N
333
S
C
N
334
N
C
N
335
N
O
N
336
N
C
N
337
N
C
N
338
N
S
N
339
N
C
N
340
N
O
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
N
N
353
S
C
N
354
N
C
N
355
N
O
N
356
N
C
Y
357
N
C
Y
358
N
C
Y
359
N
C
Y
360
N
C
Y
361
N
C
Y
362
N
C
N
363
N
O
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
N
N
376
S
C
N
377
N
C
N
378
N
O
N
379
N
C
N
380
N
C
N
381
N
C
N
382
N
O
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
N
N
393
S
C
N
394
N
C
N
395
N
O
N
396
N
C
N
397
N
O
N
398
N
O
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
H
N
403
N
H
N
404
N
H
N
405
N
H
N
406
N
N
N
407
S
C
N
408
N
C
N
409
N
O
N
410
R
C
N
411
N
O
N
412
N
C
N
413
N
O
N
414
N
H
N
415
N
H
N
416
N
H
N
417
N
H
N
418
N
H
N
419
N
H
N
420
N
H
N
421
N
H
N
422
N
H
N
423
N
N
N
424
S
C
N
425
N
C
N
426
N
O
N
427
N
C
Y
428
N
C
Y
429
N
C
Y
430
N
C
Y
431
N
N
Y
432
N
C
Y
433
N
C
Y
434
N
C
Y
435
N
C
Y
436
N
C
N
437
N
O
N
438
N
H
N
439
N
H
N
440
N
H
N
441
N
H
N
442
N
H
N
443
N
H
N
444
N
H
N
445
N
H
N
446
N
H
N
447
N
H
N
448
N
H
N
449
N
H
N
450
N
N
N
451
S
C
N
452
N
C
N
453
N
O
N
454
N
C
Y
455
N
C
Y
456
N
C
Y
457
N
C
Y
458
N
C
Y
459
N
C
Y
460
N
C
N
461
N
O
N
462
N
O
N
463
N
H
N
464
N
H
N
465
N
H
N
466
N
H
N
467
N
H
N
468
N
H
N
469
N
H
N
470
N
H
N
471
N
H
N
472
N
H
N
473
N
H
N
474
N
N
N
475
S
C
N
476
N
C
N
477
N
O
N
478
N
C
N
479
N
C
N
480
N
C
N
481
N
O
N
482
N
H
N
483
N
H
N
484
N
H
N
485
N
H
N
486
N
H
N
487
N
H
N
488
N
H
N
489
N
H
N
490
N
H
N
491
N
H
N
492
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
doub
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
doub
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
doub
N
27
N
sing
N
28
N
sing
N
29
N
doub
N
30
N
sing
N
31
N
sing
Y
32
N
sing
Y
33
N
sing
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
Y
38
N
doub
Y
39
N
doub
Y
40
N
sing
Y
41
N
sing
N
42
N
sing
Y
43
N
doub
Y
44
N
sing
Y
45
N
doub
Y
46
N
sing
Y
47
N
sing
Y
48
N
sing
Y
49
N
sing
Y
50
N
doub
Y
51
N
doub
Y
52
N
doub
Y
53
N
doub
N
54
N
sing
Y
55
N
sing
Y
56
N
doub
Y
57
N
doub
Y
58
N
sing
Y
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
doub
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
doub
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
doub
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
doub
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
doub
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
doub
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
doub
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
doub
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
doub
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
doub
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
doub
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
doub
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
doub
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
Y
247
N
sing
Y
248
N
doub
Y
249
N
doub
N
250
N
sing
Y
251
N
sing
N
252
N
sing
Y
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
doub
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
doub
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
doub
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
doub
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
doub
N
351
N
sing
N
352
N
sing
N
353
N
sing
N
354
N
sing
Y
355
N
doub
Y
356
N
sing
Y
357
N
sing
N
358
N
sing
Y
359
N
doub
N
360
N
sing
Y
361
N
doub
N
362
N
sing
Y
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
doub
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
doub
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
sing
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
sing
N
403
N
doub
N
404
N
sing
N
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
N
415
N
sing
N
416
N
sing
N
417
N
sing
N
418
N
sing
N
419
N
doub
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
sing
Y
424
N
doub
Y
425
N
sing
Y
426
N
sing
N
427
N
sing
Y
428
N
doub
Y
429
N
sing
Y
430
N
sing
N
431
N
sing
Y
432
N
sing
Y
433
N
doub
N
434
N
sing
Y
435
N
doub
N
436
N
sing
Y
437
N
sing
N
438
N
sing
N
439
N
sing
N
440
N
sing
N
441
N
sing
N
442
N
sing
N
443
N
sing
N
444
N
sing
N
445
N
sing
N
446
N
sing
N
447
N
doub
N
448
N
sing
N
449
N
sing
N
450
N
sing
N
451
N
sing
Y
452
N
doub
Y
453
N
sing
Y
454
N
sing
N
455
N
sing
Y
456
N
doub
N
457
N
sing
Y
458
N
doub
N
459
N
sing
Y
460
N
sing
N
461
N
sing
N
462
N
sing
N
463
N
sing
N
464
N
sing
N
465
N
sing
N
466
N
sing
N
467
N
sing
N
468
N
sing
N
469
N
sing
N
470
N
sing
N
471
N
doub
N
472
N
sing
N
473
N
sing
N
474
N
sing
N
475
N
sing
N
476
N
sing
N
477
N
sing
N
478
N
sing
N
479
N
sing
N
480
N
sing
N
481
N
sing
N
482
N
sing
US
J. Med. Chem.
JMCMAR
0151
1520-4804
61
5138
5153
10.1021/acs.jmedchem.7b01709
29852069
Identification of Highly Potent Human Immunodeficiency Virus Type-1 Protease Inhibitors against Lopinavir and Darunavir Resistant Viruses from Allophenylnorstatine-Based Peptidomimetics with P2 Tetrahydrofuranylglycine.
2018
10.2210/pdb5yok/pdb
pdb_00005yok
100
1
CCD
2008-07-06
RAYONIX MX225HE
SINGLE WAVELENGTH
M
x-ray
1
0.800
1.0
BL41XU
SPring-8
0.800
SYNCHROTRON
SPRING-8 BEAMLINE BL41XU
10871.872
HIV-1 PROTEASE
2
man
polymer
756.907
(4R)-N-[(2,6-dimethylphenyl)methyl]-3-[(2S,3S)-3-[[(2S)-2-[(7-methoxy-1-benzofuran-2-yl)carbonylamino]-2-[(3R)-oxolan-3 -yl]ethanoyl]amino]-2-oxidanyl-4-phenyl-butanoyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide
1
syn
non-polymer
92.094
GLYCEROL
2
syn
non-polymer
18.015
water
537
nat
water
no
no
MPQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGP
TPVNIIGRNLLTQIGATLNF
MPQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGP
TPVNIIGRNLLTQIGATLNF
A,B
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
sample
1
100
pol
11676
Human immunodeficiency virus 1
562
Escherichia coli
Biological sequence
1
2.68
54.08
VAPOR DIFFUSION, HANGING DROP
5.0
126mM phosphate buffer at pH 5.0, 63mM sodium citrate
293
chem_comp
chem_comp_atom
chem_comp_bond
database_2
entity
pdbx_entity_nonpoly
repository
Initial release
Data collection
Database references
Derived calculations
Structure summary
1
0
2018-07-18
1
1
2024-03-27
_chem_comp.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_entity.pdbx_description
_pdbx_entity_nonpoly.name
Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)
N
PDBJ
Y
PDBJ
2017-10-29
REL
REL
1
A
O
HOH
491
C
5.81
1
A
O
HOH
492
5.97
1
A
O
HOH
493
6.08
1
A
O
HOH
494
6.21
1
A
O
HOH
495
6.56
1
A
O
HOH
496
6.64
1
A
O
HOH
497
6.82
1
A
O
HOH
498
6.85
1
A
O
HOH
499
C
7.00
1
A
O
HOH
500
7.16
1
A
O
HOH
501
7.42
1
A
O
HOH
502
7.48
1
A
O
HOH
503
7.66
1
A
O
HOH
504
7.80
1
A
O
HOH
505
8.43
1
B
O
HOH
425
C
6.05
1
B
O
HOH
426
C
6.15
1
B
O
HOH
427
6.29
1
B
O
HOH
428
6.30
1
B
O
HOH
429
C
6.52
1
B
O
HOH
430
7.30
1
B
O
HOH
431
7.48
1
B
O
HOH
432
C
9.61
8Z0
(4R)-N-[(2,6-dimethylphenyl)methyl]-3-[(2S,3S)-3-[[(2S)-2-[(7-methoxy-1-benzofuran-2-yl)carbonylamino]-2-[(3R)-oxolan-3 -yl]ethanoyl]amino]-2-oxidanyl-4-phenyl-butanoyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide
GOL
GLYCEROL
HOH
water
8Z0
999
2
8Z0
8Z0
101
A
GOL
803
3
GOL
GOL
101
B
GOL
804
3
GOL
GOL
102
B
HOH
428
4
HOH
HOH
201
A
HOH
479
4
HOH
HOH
202
A
HOH
299
4
HOH
HOH
203
A
HOH
293
4
HOH
HOH
204
A
HOH
411
4
HOH
HOH
205
A
HOH
67
4
HOH
HOH
206
A
HOH
4
4
HOH
HOH
207
A
HOH
120
4
HOH
HOH
208
A
HOH
398
4
HOH
HOH
209
A
HOH
420
4
HOH
HOH
210
A
HOH
362
4
HOH
HOH
211
A
HOH
484
4
HOH
HOH
212
A
HOH
106
4
HOH
HOH
213
A
HOH
150
4
HOH
HOH
214
A
HOH
71
4
HOH
HOH
215
A
HOH
394
4
HOH
HOH
216
A
HOH
318
4
HOH
HOH
217
A
HOH
129
4
HOH
HOH
218
A
HOH
180
4
HOH
HOH
219
A
HOH
12
4
HOH
HOH
220
A
HOH
62
4
HOH
HOH
221
A
HOH
27
4
HOH
HOH
222
A
HOH
265
4
HOH
HOH
223
A
HOH
305
4
HOH
HOH
224
A
HOH
73
4
HOH
HOH
225
A
HOH
34
4
HOH
HOH
226
A
HOH
509
4
HOH
HOH
227
A
HOH
55
4
HOH
HOH
228
A
HOH
49
4
HOH
HOH
229
A
HOH
114
4
HOH
HOH
230
A
HOH
38
4
HOH
HOH
231
A
HOH
33
4
HOH
HOH
232
A
HOH
464
4
HOH
HOH
233
A
HOH
131
4
HOH
HOH
234
A
HOH
456
4
HOH
HOH
235
A
HOH
502
4
HOH
HOH
236
A
HOH
90
4
HOH
HOH
237
A
HOH
159
4
HOH
HOH
238
A
HOH
471
4
HOH
HOH
239
A
HOH
201
4
HOH
HOH
240
A
HOH
440
4
HOH
HOH
241
A
HOH
213
4
HOH
HOH
242
A
HOH
222
4
HOH
HOH
243
A
HOH
97
4
HOH
HOH
244
A
HOH
44
4
HOH
HOH
245
A
HOH
160
4
HOH
HOH
246
A
HOH
226
4
HOH
HOH
247
A
HOH
480
4
HOH
HOH
248
A
HOH
22
4
HOH
HOH
249
A
HOH
169
4
HOH
HOH
250
A
HOH
505
4
HOH
HOH
251
A
HOH
1
4
HOH
HOH
252
A
HOH
45
4
HOH
HOH
253
A
HOH
438
4
HOH
HOH
254
A
HOH
419
4
HOH
HOH
255
A
HOH
18
4
HOH
HOH
256
A
HOH
153
4
HOH
HOH
257
A
HOH
82
4
HOH
HOH
258
A
HOH
355
4
HOH
HOH
259
A
HOH
162
4
HOH
HOH
260
A
HOH
434
4
HOH
HOH
261
A
HOH
11
4
HOH
HOH
262
A
HOH
76
4
HOH
HOH
263
A
HOH
79
4
HOH
HOH
264
A
HOH
13
4
HOH
HOH
265
A
HOH
39
4
HOH
HOH
266
A
HOH
447
4
HOH
HOH
267
A
HOH
474
4
HOH
HOH
268
A
HOH
125
4
HOH
HOH
269
A
HOH
8
4
HOH
HOH
270
A
HOH
130
4
HOH
HOH
271
A
HOH
52
4
HOH
HOH
272
A
HOH
202
4
HOH
HOH
273
A
HOH
333
4
HOH
HOH
274
A
HOH
26
4
HOH
HOH
275
A
HOH
105
4
HOH
HOH
276
A
HOH
277
4
HOH
HOH
277
A
HOH
77
4
HOH
HOH
278
A
HOH
220
4
HOH
HOH
279
A
HOH
81
4
HOH
HOH
280
A
HOH
256
4
HOH
HOH
281
A
HOH
483
4
HOH
HOH
282
A
HOH
83
4
HOH
HOH
283
A
HOH
430
4
HOH
HOH
284
A
HOH
115
4
HOH
HOH
285
A
HOH
158
4
HOH
HOH
286
A
HOH
296
4
HOH
HOH
287
A
HOH
501
4
HOH
HOH
288
A
HOH
15
4
HOH
HOH
289
A
HOH
273
4
HOH
HOH
290
A
HOH
28
4
HOH
HOH
291
A
HOH
85
4
HOH
HOH
292
A
HOH
91
4
HOH
HOH
293
A
HOH
57
4
HOH
HOH
294
A
HOH
122
4
HOH
HOH
295
A
HOH
70
4
HOH
HOH
296
A
HOH
100
4
HOH
HOH
297
A
HOH
188
4
HOH
HOH
298
A
HOH
95
4
HOH
HOH
299
A
HOH
347
4
HOH
HOH
300
A
HOH
397
4
HOH
HOH
301
A
HOH
458
4
HOH
HOH
302
A
HOH
291
4
HOH
HOH
303
A
HOH
48
4
HOH
HOH
304
A
HOH
69
4
HOH
HOH
305
A
HOH
21
4
HOH
HOH
306
A
HOH
217
4
HOH
HOH
307
A
HOH
503
4
HOH
HOH
308
A
HOH
14
4
HOH
HOH
309
A
HOH
42
4
HOH
HOH
310
A
HOH
278
4
HOH
HOH
311
A
HOH
157
4
HOH
HOH
312
A
HOH
141
4
HOH
HOH
313
A
HOH
354
4
HOH
HOH
314
A
HOH
353
4
HOH
HOH
315
A
HOH
25
4
HOH
HOH
316
A
HOH
66
4
HOH
HOH
317
A
HOH
104
4
HOH
HOH
318
A
HOH
331
4
HOH
HOH
319
A
HOH
252
4
HOH
HOH
320
A
HOH
156
4
HOH
HOH
321
A
HOH
93
4
HOH
HOH
322
A
HOH
287
4
HOH
HOH
323
A
HOH
51
4
HOH
HOH
324
A
HOH
16
4
HOH
HOH
325
A
HOH
251
4
HOH
HOH
326
A
HOH
489
4
HOH
HOH
327
A
HOH
337
4
HOH
HOH
328
A
HOH
350
4
HOH
HOH
329
A
HOH
212
4
HOH
HOH
330
A
HOH
506
4
HOH
HOH
331
A
HOH
102
4
HOH
HOH
332
A
HOH
439
4
HOH
HOH
333
A
HOH
237
4
HOH
HOH
334
A
HOH
348
4
HOH
HOH
335
A
HOH
492
4
HOH
HOH
336
A
HOH
210
4
HOH
HOH
337
A
HOH
429
4
HOH
HOH
338
A
HOH
528
4
HOH
HOH
339
A
HOH
260
4
HOH
HOH
340
A
HOH
136
4
HOH
HOH
341
A
HOH
450
4
HOH
HOH
342
A
HOH
306
4
HOH
HOH
343
A
HOH
171
4
HOH
HOH
344
A
HOH
142
4
HOH
HOH
345
A
HOH
233
4
HOH
HOH
346
A
HOH
472
4
HOH
HOH
347
A
HOH
406
4
HOH
HOH
348
A
HOH
403
4
HOH
HOH
349
A
HOH
488
4
HOH
HOH
350
A
HOH
190
4
HOH
HOH
351
A
HOH
514
4
HOH
HOH
352
A
HOH
382
4
HOH
HOH
353
A
HOH
326
4
HOH
HOH
354
A
HOH
425
4
HOH
HOH
355
A
HOH
257
4
HOH
HOH
356
A
HOH
227
4
HOH
HOH
357
A
HOH
357
4
HOH
HOH
358
A
HOH
68
4
HOH
HOH
359
A
HOH
504
4
HOH
HOH
360
A
HOH
176
4
HOH
HOH
361
A
HOH
373
4
HOH
HOH
362
A
HOH
379
4
HOH
HOH
363
A
HOH
279
4
HOH
HOH
364
A
HOH
446
4
HOH
HOH
365
A
HOH
99
4
HOH
HOH
366
A
HOH
507
4
HOH
HOH
367
A
HOH
165
4
HOH
HOH
368
A
HOH
243
4
HOH
HOH
369
A
HOH
191
4
HOH
HOH
370
A
HOH
448
4
HOH
HOH
371
A
HOH
276
4
HOH
HOH
372
A
HOH
535
4
HOH
HOH
373
A
HOH
457
4
HOH
HOH
374
A
HOH
310
4
HOH
HOH
375
A
HOH
335
4
HOH
HOH
376
A
HOH
239
4
HOH
HOH
377
A
HOH
443
4
HOH
HOH
378
A
HOH
206
4
HOH
HOH
379
A
HOH
177
4
HOH
HOH
380
A
HOH
399
4
HOH
HOH
381
A
HOH
263
4
HOH
HOH
382
A
HOH
371
4
HOH
HOH
383
A
HOH
302
4
HOH
HOH
384
A
HOH
378
4
HOH
HOH
385
A
HOH
431
4
HOH
HOH
386
A
HOH
536
4
HOH
HOH
387
A
HOH
473
4
HOH
HOH
388
A
HOH
301
4
HOH
HOH
389
A
HOH
193
4
HOH
HOH
390
A
HOH
330
4
HOH
HOH
391
A
HOH
267
4
HOH
HOH
392
A
HOH
369
4
HOH
HOH
393
A
HOH
338
4
HOH
HOH
394
A
HOH
179
4
HOH
HOH
395
A
HOH
516
4
HOH
HOH
396
A
HOH
59
4
HOH
HOH
397
A
HOH
204
4
HOH
HOH
398
A
HOH
272
4
HOH
HOH
399
A
HOH
173
4
HOH
HOH
400
A
HOH
288
4
HOH
HOH
401
A
HOH
111
4
HOH
HOH
402
A
HOH
133
4
HOH
HOH
403
A
HOH
400
4
HOH
HOH
404
A
HOH
147
4
HOH
HOH
405
A
HOH
74
4
HOH
HOH
406
A
HOH
166
4
HOH
HOH
407
A
HOH
485
4
HOH
HOH
408
A
HOH
207
4
HOH
HOH
409
A
HOH
407
4
HOH
HOH
410
A
HOH
282
4
HOH
HOH
411
A
HOH
155
4
HOH
HOH
412
A
HOH
247
4
HOH
HOH
413
A
HOH
185
4
HOH
HOH
414
A
HOH
234
4
HOH
HOH
415
A
HOH
323
4
HOH
HOH
416
A
HOH
192
4
HOH
HOH
417
A
HOH
135
4
HOH
HOH
418
A
HOH
468
4
HOH
HOH
419
A
HOH
56
4
HOH
HOH
420
A
HOH
360
4
HOH
HOH
421
A
HOH
459
4
HOH
HOH
422
A
HOH
452
4
HOH
HOH
423
A
HOH
436
4
HOH
HOH
424
A
HOH
334
4
HOH
HOH
425
A
HOH
238
4
HOH
HOH
426
A
HOH
161
4
HOH
HOH
427
A
HOH
493
4
HOH
HOH
428
A
HOH
365
4
HOH
HOH
429
A
HOH
376
4
HOH
HOH
430
A
HOH
324
4
HOH
HOH
431
A
HOH
283
4
HOH
HOH
432
A
HOH
126
4
HOH
HOH
433
A
HOH
435
4
HOH
HOH
434
A
HOH
368
4
HOH
HOH
435
A
HOH
432
4
HOH
HOH
436
A
HOH
391
4
HOH
HOH
437
A
HOH
297
4
HOH
HOH
438
A
HOH
385
4
HOH
HOH
439
A
HOH
151
4
HOH
HOH
440
A
HOH
286
4
HOH
HOH
441
A
HOH
517
4
HOH
HOH
442
A
HOH
396
4
HOH
HOH
443
A
HOH
285
4
HOH
HOH
444
A
HOH
401
4
HOH
HOH
445
A
HOH
358
4
HOH
HOH
446
A
HOH
381
4
HOH
HOH
447
A
HOH
107
4
HOH
HOH
448
A
HOH
194
4
HOH
HOH
449
A
HOH
386
4
HOH
HOH
450
A
HOH
269
4
HOH
HOH
451
A
HOH
416
4
HOH
HOH
452
A
HOH
487
4
HOH
HOH
453
A
HOH
266
4
HOH
HOH
454
A
HOH
470
4
HOH
HOH
455
A
HOH
108
4
HOH
HOH
456
A
HOH
197
4
HOH
HOH
457
A
HOH
412
4
HOH
HOH
458
A
HOH
75
4
HOH
HOH
459
A
HOH
414
4
HOH
HOH
460
A
HOH
230
4
HOH
HOH
461
A
HOH
170
4
HOH
HOH
462
A
HOH
345
4
HOH
HOH
463
A
HOH
134
4
HOH
HOH
464
A
HOH
292
4
HOH
HOH
465
A
HOH
409
4
HOH
HOH
466
A
HOH
148
4
HOH
HOH
467
A
HOH
187
4
HOH
HOH
468
A
HOH
393
4
HOH
HOH
469
A
HOH
522
4
HOH
HOH
470
A
HOH
366
4
HOH
HOH
471
A
HOH
367
4
HOH
HOH
472
A
HOH
415
4
HOH
HOH
473
A
HOH
496
4
HOH
HOH
474
A
HOH
58
4
HOH
HOH
475
A
HOH
529
4
HOH
HOH
476
A
HOH
336
4
HOH
HOH
477
A
HOH
372
4
HOH
HOH
478
A
HOH
307
4
HOH
HOH
479
A
HOH
523
4
HOH
HOH
480
A
HOH
119
4
HOH
HOH
481
A
HOH
377
4
HOH
HOH
482
A
HOH
351
4
HOH
HOH
483
A
HOH
46
4
HOH
HOH
484
A
HOH
321
4
HOH
HOH
485
A
HOH
205
4
HOH
HOH
486
A
HOH
410
4
HOH
HOH
487
A
HOH
389
4
HOH
HOH
488
A
HOH
132
4
HOH
HOH
489
A
HOH
244
4
HOH
HOH
490
A
HOH
515
4
HOH
HOH
491
A
HOH
356
4
HOH
HOH
492
A
HOH
271
4
HOH
HOH
493
A
HOH
421
4
HOH
HOH
494
A
HOH
451
4
HOH
HOH
495
A
HOH
289
4
HOH
HOH
496
A
HOH
281
4
HOH
HOH
497
A
HOH
370
4
HOH
HOH
498
A
HOH
534
4
HOH
HOH
499
A
HOH
172
4
HOH
HOH
500
A
HOH
402
4
HOH
HOH
501
A
HOH
352
4
HOH
HOH
502
A
HOH
418
4
HOH
HOH
503
A
HOH
316
4
HOH
HOH
504
A
HOH
424
4
HOH
HOH
505
A
HOH
319
4
HOH
HOH
201
B
HOH
476
4
HOH
HOH
202
B
HOH
315
4
HOH
HOH
203
B
HOH
86
4
HOH
HOH
204
B
HOH
246
4
HOH
HOH
205
B
HOH
139
4
HOH
HOH
206
B
HOH
41
4
HOH
HOH
207
B
HOH
512
4
HOH
HOH
208
B
HOH
200
4
HOH
HOH
209
B
HOH
218
4
HOH
HOH
210
B
HOH
408
4
HOH
HOH
211
B
HOH
231
4
HOH
HOH
212
B
HOH
405
4
HOH
HOH
213
B
HOH
486
4
HOH
HOH
214
B
HOH
304
4
HOH
HOH
215
B
HOH
361
4
HOH
HOH
216
B
HOH
463
4
HOH
HOH
217
B
HOH
178
4
HOH
HOH
218
B
HOH
426
4
HOH
HOH
219
B
HOH
312
4
HOH
HOH
220
B
HOH
259
4
HOH
HOH
221
B
HOH
241
4
HOH
HOH
222
B
HOH
96
4
HOH
HOH
223
B
HOH
43
4
HOH
HOH
224
B
HOH
437
4
HOH
HOH
225
B
HOH
23
4
HOH
HOH
226
B
HOH
465
4
HOH
HOH
227
B
HOH
388
4
HOH
HOH
228
B
HOH
124
4
HOH
HOH
229
B
HOH
510
4
HOH
HOH
230
B
HOH
116
4
HOH
HOH
231
B
HOH
17
4
HOH
HOH
232
B
HOH
339
4
HOH
HOH
233
B
HOH
380
4
HOH
HOH
234
B
HOH
118
4
HOH
HOH
235
B
HOH
19
4
HOH
HOH
236
B
HOH
413
4
HOH
HOH
237
B
HOH
325
4
HOH
HOH
238
B
HOH
242
4
HOH
HOH
239
B
HOH
290
4
HOH
HOH
240
B
HOH
494
4
HOH
HOH
241
B
HOH
433
4
HOH
HOH
242
B
HOH
214
4
HOH
HOH
243
B
HOH
219
4
HOH
HOH
244
B
HOH
254
4
HOH
HOH
245
B
HOH
511
4
HOH
HOH
246
B
HOH
327
4
HOH
HOH
247
B
HOH
163
4
HOH
HOH
248
B
HOH
183
4
HOH
HOH
249
B
HOH
20
4
HOH
HOH
250
B
HOH
184
4
HOH
HOH
251
B
HOH
264
4
HOH
HOH
252
B
HOH
32
4
HOH
HOH
253
B
HOH
9
4
HOH
HOH
254
B
HOH
225
4
HOH
HOH
255
B
HOH
78
4
HOH
HOH
256
B
HOH
392
4
HOH
HOH
257
B
HOH
303
4
HOH
HOH
258
B
HOH
2
4
HOH
HOH
259
B
HOH
235
4
HOH
HOH
260
B
HOH
65
4
HOH
HOH
261
B
HOH
138
4
HOH
HOH
262
B
HOH
60
4
HOH
HOH
263
B
HOH
274
4
HOH
HOH
264
B
HOH
284
4
HOH
HOH
265
B
HOH
145
4
HOH
HOH
266
B
HOH
92
4
HOH
HOH
267
B
HOH
110
4
HOH
HOH
268
B
HOH
475
4
HOH
HOH
269
B
HOH
215
4
HOH
HOH
270
B
HOH
154
4
HOH
HOH
271
B
HOH
498
4
HOH
HOH
272
B
HOH
152
4
HOH
HOH
273
B
HOH
29
4
HOH
HOH
274
B
HOH
209
4
HOH
HOH
275
B
HOH
149
4
HOH
HOH
276
B
HOH
198
4
HOH
HOH
277
B
HOH
519
4
HOH
HOH
278
B
HOH
3
4
HOH
HOH
279
B
HOH
10
4
HOH
HOH
280
B
HOH
144
4
HOH
HOH
281
B
HOH
383
4
HOH
HOH
282
B
HOH
101
4
HOH
HOH
283
B
HOH
203
4
HOH
HOH
284
B
HOH
320
4
HOH
HOH
285
B
HOH
35
4
HOH
HOH
286
B
HOH
311
4
HOH
HOH
287
B
HOH
199
4
HOH
HOH
288
B
HOH
229
4
HOH
HOH
289
B
HOH
61
4
HOH
HOH
290
B
HOH
6
4
HOH
HOH
291
B
HOH
47
4
HOH
HOH
292
B
HOH
31
4
HOH
HOH
293
B
HOH
88
4
HOH
HOH
294
B
HOH
168
4
HOH
HOH
295
B
HOH
63
4
HOH
HOH
296
B
HOH
490
4
HOH
HOH
297
B
HOH
36
4
HOH
HOH
298
B
HOH
181
4
HOH
HOH
299
B
HOH
137
4
HOH
HOH
300
B
HOH
40
4
HOH
HOH
301
B
HOH
499
4
HOH
HOH
302
B
HOH
50
4
HOH
HOH
303
B
HOH
53
4
HOH
HOH
304
B
HOH
208
4
HOH
HOH
305
B
HOH
89
4
HOH
HOH
306
B
HOH
84
4
HOH
HOH
307
B
HOH
30
4
HOH
HOH
308
B
HOH
232
4
HOH
HOH
309
B
HOH
216
4
HOH
HOH
310
B
HOH
121
4
HOH
HOH
311
B
HOH
5
4
HOH
HOH
312
B
HOH
491
4
HOH
HOH
313
B
HOH
87
4
HOH
HOH
314
B
HOH
462
4
HOH
HOH
315
B
HOH
167
4
HOH
HOH
316
B
HOH
72
4
HOH
HOH
317
B
HOH
518
4
HOH
HOH
318
B
HOH
109
4
HOH
HOH
319
B
HOH
481
4
HOH
HOH
320
B
HOH
174
4
HOH
HOH
321
B
HOH
24
4
HOH
HOH
322
B
HOH
341
4
HOH
HOH
323
B
HOH
404
4
HOH
HOH
324
B
HOH
64
4
HOH
HOH
325
B
HOH
196
4
HOH
HOH
326
B
HOH
445
4
HOH
HOH
327
B
HOH
228
4
HOH
HOH
328
B
HOH
359
4
HOH
HOH
329
B
HOH
497
4
HOH
HOH
330
B
HOH
7
4
HOH
HOH
331
B
HOH
525
4
HOH
HOH
332
B
HOH
261
4
HOH
HOH
333
B
HOH
314
4
HOH
HOH
334
B
HOH
280
4
HOH
HOH
335
B
HOH
478
4
HOH
HOH
336
B
HOH
455
4
HOH
HOH
337
B
HOH
395
4
HOH
HOH
338
B
HOH
123
4
HOH
HOH
339
B
HOH
532
4
HOH
HOH
340
B
HOH
374
4
HOH
HOH
341
B
HOH
294
4
HOH
HOH
342
B
HOH
103
4
HOH
HOH
343
B
HOH
112
4
HOH
HOH
344
B
HOH
189
4
HOH
HOH
345
B
HOH
417
4
HOH
HOH
346
B
HOH
495
4
HOH
HOH
347
B
HOH
375
4
HOH
HOH
348
B
HOH
258
4
HOH
HOH
349
B
HOH
461
4
HOH
HOH
350
B
HOH
127
4
HOH
HOH
351
B
HOH
467
4
HOH
HOH
352
B
HOH
236
4
HOH
HOH
353
B
HOH
500
4
HOH
HOH
354
B
HOH
308
4
HOH
HOH
355
B
HOH
94
4
HOH
HOH
356
B
HOH
182
4
HOH
HOH
357
B
HOH
482
4
HOH
HOH
358
B
HOH
387
4
HOH
HOH
359
B
HOH
255
4
HOH
HOH
360
B
HOH
54
4
HOH
HOH
361
B
HOH
524
4
HOH
HOH
362
B
HOH
140
4
HOH
HOH
363
B
HOH
143
4
HOH
HOH
364
B
HOH
253
4
HOH
HOH
365
B
HOH
175
4
HOH
HOH
366
B
HOH
317
4
HOH
HOH
367
B
HOH
268
4
HOH
HOH
368
B
HOH
164
4
HOH
HOH
369
B
HOH
117
4
HOH
HOH
370
B
HOH
349
4
HOH
HOH
371
B
HOH
328
4
HOH
HOH
372
B
HOH
460
4
HOH
HOH
373
B
HOH
270
4
HOH
HOH
374
B
HOH
526
4
HOH
HOH
375
B
HOH
113
4
HOH
HOH
376
B
HOH
477
4
HOH
HOH
377
B
HOH
240
4
HOH
HOH
378
B
HOH
128
4
HOH
HOH
379
B
HOH
384
4
HOH
HOH
380
B
HOH
186
4
HOH
HOH
381
B
HOH
344
4
HOH
HOH
382
B
HOH
513
4
HOH
HOH
383
B
HOH
444
4
HOH
HOH
384
B
HOH
442
4
HOH
HOH
385
B
HOH
340
4
HOH
HOH
386
B
HOH
441
4
HOH
HOH
387
B
HOH
80
4
HOH
HOH
388
B
HOH
262
4
HOH
HOH
389
B
HOH
346
4
HOH
HOH
390
B
HOH
300
4
HOH
HOH
391
B
HOH
363
4
HOH
HOH
392
B
HOH
322
4
HOH
HOH
393
B
HOH
332
4
HOH
HOH
394
B
HOH
248
4
HOH
HOH
395
B
HOH
298
4
HOH
HOH
396
B
HOH
295
4
HOH
HOH
397
B
HOH
37
4
HOH
HOH
398
B
HOH
508
4
HOH
HOH
399
B
HOH
466
4
HOH
HOH
400
B
HOH
422
4
HOH
HOH
401
B
HOH
146
4
HOH
HOH
402
B
HOH
245
4
HOH
HOH
403
B
HOH
250
4
HOH
HOH
404
B
HOH
221
4
HOH
HOH
405
B
HOH
390
4
HOH
HOH
406
B
HOH
313
4
HOH
HOH
407
B
HOH
249
4
HOH
HOH
408
B
HOH
423
4
HOH
HOH
409
B
HOH
224
4
HOH
HOH
410
B
HOH
98
4
HOH
HOH
411
B
HOH
520
4
HOH
HOH
412
B
HOH
342
4
HOH
HOH
413
B
HOH
427
4
HOH
HOH
414
B
HOH
449
4
HOH
HOH
415
B
HOH
533
4
HOH
HOH
416
B
HOH
275
4
HOH
HOH
417
B
HOH
329
4
HOH
HOH
418
B
HOH
453
4
HOH
HOH
419
B
HOH
537
4
HOH
HOH
420
B
HOH
454
4
HOH
HOH
421
B
HOH
364
4
HOH
HOH
422
B
HOH
223
4
HOH
HOH
423
B
HOH
211
4
HOH
HOH
424
B
HOH
531
4
HOH
HOH
425
B
HOH
521
4
HOH
HOH
426
B
HOH
343
4
HOH
HOH
427
B
HOH
195
4
HOH
HOH
428
B
HOH
530
4
HOH
HOH
429
B
HOH
309
4
HOH
HOH
430
B
HOH
469
4
HOH
HOH
431
B
HOH
527
4
HOH
HOH
432
B
n
1
0
A
PRO
1
n
2
PRO
1
A
GLN
2
n
3
GLN
2
A
ILE
3
n
4
ILE
3
A
THR
4
n
5
THR
4
A
LEU
5
n
6
LEU
5
A
TRP
6
n
7
TRP
6
A
LYS
7
n
8
LYS
7
A
ARG
8
n
9
ARG
8
A
PRO
9
n
10
PRO
9
A
LEU
10
n
11
LEU
10
A
VAL
11
n
12
VAL
11
A
THR
12
n
13
THR
12
A
ILE
13
n
14
ILE
13
A
LYS
14
n
15
LYS
14
A
ILE
15
n
16
ILE
15
A
GLY
16
n
17
GLY
16
A
GLY
17
n
18
GLY
17
A
GLN
18
n
19
GLN
18
A
LEU
19
n
20
LEU
19
A
LYS
20
n
21
LYS
20
A
GLU
21
n
22
GLU
21
A
ALA
22
n
23
ALA
22
A
LEU
23
n
24
LEU
23
A
LEU
24
n
25
LEU
24
A
ASP
25
n
26
ASP
25
A
THR
26
n
27
THR
26
A
GLY
27
n
28
GLY
27
A
ALA
28
n
29
ALA
28
A
ASP
29
n
30
ASP
29
A
ASP
30
n
31
ASP
30
A
THR
31
n
32
THR
31
A
VAL
32
n
33
VAL
32
A
ILE
33
n
34
ILE
33
A
GLU
34
n
35
GLU
34
A
GLU
35
n
36
GLU
35
A
MET
36
n
37
MET
36
A
SER
37
n
38
SER
37
A
LEU
38
n
39
LEU
38
A
PRO
39
n
40
PRO
39
A
GLY
40
n
41
GLY
40
A
ARG
41
n
42
ARG
41
A
TRP
42
n
43
TRP
42
A
LYS
43
n
44
LYS
43
A
PRO
44
n
45
PRO
44
A
LYS
45
n
46
LYS
45
A
MET
46
n
47
MET
46
A
ILE
47
n
48
ILE
47
A
GLY
48
n
49
GLY
48
A
GLY
49
n
50
GLY
49
A
ILE
50
n
51
ILE
50
A
GLY
51
n
52
GLY
51
A
GLY
52
n
53
GLY
52
A
PHE
53
n
54
PHE
53
A
ILE
54
n
55
ILE
54
A
LYS
55
n
56
LYS
55
A
VAL
56
n
57
VAL
56
A
ARG
57
n
58
ARG
57
A
GLN
58
n
59
GLN
58
A
TYR
59
n
60
TYR
59
A
ASP
60
n
61
ASP
60
A
GLN
61
n
62
GLN
61
A
ILE
62
n
63
ILE
62
A
ILE
63
n
64
ILE
63
A
ILE
64
n
65
ILE
64
A
GLU
65
n
66
GLU
65
A
ILE
66
n
67
ILE
66
A
ALA
67
n
68
ALA
67
A
GLY
68
n
69
GLY
68
A
HIS
69
n
70
HIS
69
A
LYS
70
n
71
LYS
70
A
ALA
71
n
72
ALA
71
A
ILE
72
n
73
ILE
72
A
GLY
73
n
74
GLY
73
A
THR
74
n
75
THR
74
A
VAL
75
n
76
VAL
75
A
LEU
76
n
77
LEU
76
A
VAL
77
n
78
VAL
77
A
GLY
78
n
79
GLY
78
A
PRO
79
n
80
PRO
79
A
THR
80
n
81
THR
80
A
PRO
81
n
82
PRO
81
A
VAL
82
n
83
VAL
82
A
ASN
83
n
84
ASN
83
A
ILE
84
n
85
ILE
84
A
ILE
85
n
86
ILE
85
A
GLY
86
n
87
GLY
86
A
ARG
87
n
88
ARG
87
A
ASN
88
n
89
ASN
88
A
LEU
89
n
90
LEU
89
A
LEU
90
n
91
LEU
90
A
THR
91
n
92
THR
91
A
GLN
92
n
93
GLN
92
A
ILE
93
n
94
ILE
93
A
GLY
94
n
95
GLY
94
A
ALA
95
n
96
ALA
95
A
THR
96
n
97
THR
96
A
LEU
97
n
98
LEU
97
A
ASN
98
n
99
ASN
98
A
PHE
99
n
100
PHE
99
A
n
1
0
B
PRO
1
n
2
PRO
1
B
GLN
2
n
3
GLN
2
B
ILE
3
n
4
ILE
3
B
THR
4
n
5
THR
4
B
LEU
5
n
6
LEU
5
B
TRP
6
n
7
TRP
6
B
LYS
7
n
8
LYS
7
B
ARG
8
n
9
ARG
8
B
PRO
9
n
10
PRO
9
B
LEU
10
n
11
LEU
10
B
VAL
11
n
12
VAL
11
B
THR
12
n
13
THR
12
B
ILE
13
n
14
ILE
13
B
LYS
14
n
15
LYS
14
B
ILE
15
n
16
ILE
15
B
GLY
16
n
17
GLY
16
B
GLY
17
n
18
GLY
17
B
GLN
18
n
19
GLN
18
B
LEU
19
n
20
LEU
19
B
LYS
20
n
21
LYS
20
B
GLU
21
n
22
GLU
21
B
ALA
22
n
23
ALA
22
B
LEU
23
n
24
LEU
23
B
LEU
24
n
25
LEU
24
B
ASP
25
n
26
ASP
25
B
THR
26
n
27
THR
26
B
GLY
27
n
28
GLY
27
B
ALA
28
n
29
ALA
28
B
ASP
29
n
30
ASP
29
B
ASP
30
n
31
ASP
30
B
THR
31
n
32
THR
31
B
VAL
32
n
33
VAL
32
B
ILE
33
n
34
ILE
33
B
GLU
34
n
35
GLU
34
B
GLU
35
n
36
GLU
35
B
MET
36
n
37
MET
36
B
SER
37
n
38
SER
37
B
LEU
38
n
39
LEU
38
B
PRO
39
n
40
PRO
39
B
GLY
40
n
41
GLY
40
B
ARG
41
n
42
ARG
41
B
TRP
42
n
43
TRP
42
B
LYS
43
n
44
LYS
43
B
PRO
44
n
45
PRO
44
B
LYS
45
n
46
LYS
45
B
MET
46
n
47
MET
46
B
ILE
47
n
48
ILE
47
B
GLY
48
n
49
GLY
48
B
GLY
49
n
50
GLY
49
B
ILE
50
n
51
ILE
50
B
GLY
51
n
52
GLY
51
B
GLY
52
n
53
GLY
52
B
PHE
53
n
54
PHE
53
B
ILE
54
n
55
ILE
54
B
LYS
55
n
56
LYS
55
B
VAL
56
n
57
VAL
56
B
ARG
57
n
58
ARG
57
B
GLN
58
n
59
GLN
58
B
TYR
59
n
60
TYR
59
B
ASP
60
n
61
ASP
60
B
GLN
61
n
62
GLN
61
B
ILE
62
n
63
ILE
62
B
ILE
63
n
64
ILE
63
B
ILE
64
n
65
ILE
64
B
GLU
65
n
66
GLU
65
B
ILE
66
n
67
ILE
66
B
ALA
67
n
68
ALA
67
B
GLY
68
n
69
GLY
68
B
HIS
69
n
70
HIS
69
B
LYS
70
n
71
LYS
70
B
ALA
71
n
72
ALA
71
B
ILE
72
n
73
ILE
72
B
GLY
73
n
74
GLY
73
B
THR
74
n
75
THR
74
B
VAL
75
n
76
VAL
75
B
LEU
76
n
77
LEU
76
B
VAL
77
n
78
VAL
77
B
GLY
78
n
79
GLY
78
B
PRO
79
n
80
PRO
79
B
THR
80
n
81
THR
80
B
PRO
81
n
82
PRO
81
B
VAL
82
n
83
VAL
82
B
ASN
83
n
84
ASN
83
B
ILE
84
n
85
ILE
84
B
ILE
85
n
86
ILE
85
B
GLY
86
n
87
GLY
86
B
ARG
87
n
88
ARG
87
B
ASN
88
n
89
ASN
88
B
LEU
89
n
90
LEU
89
B
LEU
90
n
91
LEU
90
B
THR
91
n
92
THR
91
B
GLN
92
n
93
GLN
92
B
ILE
93
n
94
ILE
93
B
GLY
94
n
95
GLY
94
B
ALA
95
n
96
ALA
95
B
THR
96
n
97
THR
96
B
LEU
97
n
98
LEU
97
B
ASN
98
n
99
ASN
98
B
PHE
99
n
100
PHE
99
B
0.097
0.103
0.118
0.125
9062
10024
5.0
5.0
181768
author_and_software_defined_assembly
PISA
2
dimeric
gel filtration
4500
-24
9550
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
ILE
3
A
N
ILE
4
B
O
LEU
97
B
O
LEU
98
B
O
THR
96
B
O
THR
97
A
N
ASN
98
A
N
ASN
99
A
N
LEU
97
A
N
LEU
98
B
O
ILE
3
B
O
ILE
4
A
N
LYS
43
A
N
LYS
44
A
O
GLN
58
A
O
GLN
59
A
N
ILE
66
A
N
ILE
67
A
O
HIS
69
A
O
HIS
70
A
O
LEU
76
A
O
LEU
77
A
N
ILE
33
A
N
ILE
34
A
N
VAL
32
A
N
VAL
33
A
O
ILE
84
A
O
ILE
85
A
O
ILE
85
A
O
ILE
86
A
N
LEU
23
A
N
LEU
24
A
O
LYS
20
A
O
LYS
21
A
N
ILE
13
A
N
ILE
14
A
N
LYS
14
A
N
LYS
15
A
O
GLU
65
A
O
GLU
66
B
N
GLY
49
B
N
GLY
50
B
O
GLY
52
B
O
GLY
53
B
N
ILE
66
B
N
ILE
67
B
O
HIS
69
B
O
HIS
70
B
O
LEU
76
B
O
LEU
77
B
N
ILE
33
B
N
ILE
34
B
N
VAL
32
B
N
VAL
33
B
O
ILE
84
B
O
ILE
85
B
O
ILE
85
B
O
ILE
86
B
N
LEU
23
B
N
LEU
24
B
O
LYS
20
B
O
LYS
21
B
N
ILE
13
B
N
ILE
14
B
N
LYS
14
B
N
LYS
15
B
O
GLU
65
B
O
GLU
66
1
A
HOH
393
F
HOH
1
A
HOH
413
F
HOH
1
A
MET
0
A
MET
1
1
Y
1
B
MET
0
B
MET
1
1
Y
1
B
B
OD1
O
ASP
HOH
30
201
1.37
B
1
B
B
HE3
O
LYS
HOH
43
247
1.54
B
1
A
A
O
O
HOH
HOH
290
428
1.58
B
1
B
B
O
O
HOH
HOH
266
340
1.59
C
1
B
B
O
O
HOH
HOH
416
418
1.74
C
1
A
A
O
O
ILE
HOH
50
203
1.80
B
1
B
B
O
O
HOH
HOH
208
349
1.84
B
1
B
B
CG
O
ASP
HOH
30
201
2.03
B
1
A
ILE
62
-15.20
1
6.66
0.50
120.30
126.96
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
41
41
41
N
1
17.23
2.30
111.70
128.93
A
A
A
CD
CE
NZ
LYS
LYS
LYS
45
45
45
N
1
13.48
1.40
123.60
137.08
A
A
A
CD
NE
CZ
ARG
ARG
ARG
57
57
57
A
A
A
N
1
-13.46
1.60
122.70
109.24
A
A
A
O
C
N
ILE
ILE
ILE
62
62
63
A
Y
1
-13.69
1.90
110.20
96.51
A
A
A
CB
CA
C
LEU
LEU
LEU
97
97
97
A
N
1
12.84
1.90
110.20
123.04
A
A
A
CB
CA
C
LEU
LEU
LEU
97
97
97
B
N
1
17.21
2.40
116.70
133.91
B
B
B
CG
CD
NE2
GLN
GLN
GLN
2
2
2
N
1
-8.37
0.90
118.30
109.93
B
B
B
CB
CG
OD1
ASP
ASP
ASP
25
25
25
B
B
N
1
14.49
2.20
113.40
127.89
B
B
B
CA
CB
CG
LYS
LYS
LYS
43
43
43
B
N
1
17.82
2.60
111.60
129.42
B
B
B
CB
CG
CD
LYS
LYS
LYS
45
45
45
A
A
A
N
1
23.77
3.00
111.90
135.67
B
B
B
CG
CD
CE
LYS
LYS
LYS
45
45
45
A
A
A
N
1
-10.44
1.60
100.20
89.76
B
B
B
CG
SD
CE
MET
MET
MET
46
46
46
B
B
B
N
1
17.45
2.10
122.30
139.75
B
B
B
C
N
CA
GLY
GLY
GLY
48
49
49
B
B
B
Y
1
7.86
1.20
123.30
131.16
B
B
B
OE1
CD
OE2
GLU
GLU
GLU
65
65
65
B
B
B
N
1
A
A
CZ
NH1
ARG
ARG
57
57
0.115
0.013
1.326
1.441
A
A
N
1
A
A
CD
OE2
GLU
GLU
65
65
-0.067
0.011
1.252
1.185
N
1
B
B
CB
CG1
ILE
ILE
33
33
-0.196
0.028
1.536
1.340
A
N
1
B
B
CB
CG
GLU
GLU
65
65
-0.164
0.019
1.517
1.353
B
N
1
A
B
O
O
HOH
HOH
237
416
1.58
C
1_555
3_556
1
B
GLU
35
B
-38.93
125.98
16.0248
0.125
0.103
0.103
0.85
34.6
10024
200529
181768
1
FREE R-VALUE
FOURIER SYNTHESIS
0.85
34.6
537
2115
66
0
1512
0.016
2.130
0.850
34.600
5YOK
200529
0.06200
1
50.4000
11.10
97.9
0.33100
0.85
0.88
3.000
1
5.10
89.8
refinement
SHELXL
data reduction
HKL-2000
data scaling
SCALA
phasing
PHENIX
N
Structure of HIV-1 Protease in Complex with Inhibitor KNI-1657
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
4
N
N
4
N
N
A
GLY
86
A
GLY
87
HELX_P
A
THR
91
A
THR
92
1
AA1
6
B
GLY
86
B
GLY
87
HELX_P
B
THR
91
B
THR
92
1
AA2
6
HYDROLASE/HYDROLASE INHIBITOR
inhibitor, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex
5YOK
PDB
1
1
5YOK
0
99
5YOK
0
99
5YOK
A
1
1
100
0
99
5YOK
0
99
5YOK
B
1
1
100
4
8
8
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
GLN
2
A
GLN
3
A
ILE
3
A
ILE
4
B
THR
96
B
THR
97
B
ASN
98
B
ASN
99
A
THR
96
A
THR
97
A
ASN
98
A
ASN
99
B
GLN
2
B
GLN
3
B
ILE
3
B
ILE
4
A
TRP
42
A
TRP
43
A
GLY
49
A
GLY
50
A
GLY
52
A
GLY
53
A
ILE
66
A
ILE
67
A
HIS
69
A
HIS
70
A
VAL
77
A
VAL
78
A
VAL
32
A
VAL
33
A
ILE
33
A
ILE
34
A
ILE
84
A
ILE
85
A
ILE
85
A
ILE
86
A
GLN
18
A
GLN
19
A
LEU
24
A
LEU
25
A
LEU
10
A
LEU
11
A
ILE
15
A
ILE
16
A
GLY
52
A
GLY
53
A
ILE
66
A
ILE
67
B
LYS
43
B
LYS
44
B
GLY
49
B
GLY
50
B
GLY
52
B
GLY
53
B
ILE
66
B
ILE
67
B
HIS
69
B
HIS
70
B
VAL
77
B
VAL
78
B
VAL
32
B
VAL
33
B
ILE
33
B
ILE
34
B
ILE
84
B
ILE
85
B
ILE
85
B
ILE
86
B
GLN
18
B
GLN
19
B
LEU
24
B
LEU
25
B
LEU
10
B
LEU
11
B
ILE
15
B
ILE
16
B
GLY
52
B
GLY
53
B
ILE
66
B
ILE
67
binding site for residue 8Z0 A 101
A
8Z0
101
Software
44
binding site for residue GOL B 101
B
GOL
101
Software
12
binding site for residue GOL B 102
B
GOL
102
Software
8
A
TRP
6
A
TRP
7
44
4_556
A
ARG
8
A
ARG
9
44
1_555
A
LEU
23
A
LEU
24
44
1_555
A
ASP
25
A
ASP
26
44
1_555
A
GLY
27
A
GLY
28
44
1_555
A
ALA
28
A
ALA
29
44
1_555
A
ASP
29
A
ASP
30
44
1_555
A
ASP
30
A
ASP
31
44
1_555
A
GLY
48
A
GLY
49
44
1_555
A
GLY
49
A
GLY
50
44
1_555
A
ILE
50
A
ILE
51
44
1_555
A
PRO
81
A
PRO
82
44
1_555
A
VAL
82
A
VAL
83
44
1_555
A
ILE
84
A
ILE
85
44
1_555
A
HOH
202
F
HOH
44
1_555
A
HOH
207
F
HOH
44
1_555
A
HOH
212
F
HOH
44
1_555
A
HOH
220
F
HOH
44
1_555
A
HOH
247
F
HOH
44
1_555
A
HOH
248
F
HOH
44
1_555
A
HOH
282
F
HOH
44
1_555
A
HOH
288
F
HOH
44
1_555
A
HOH
308
F
HOH
44
1_555
A
HOH
367
F
HOH
44
1_555
A
HOH
442
F
HOH
44
1_555
A
HOH
499
F
HOH
44
4_556
B
ARG
8
B
ARG
9
44
1_555
B
LEU
23
B
LEU
24
44
1_555
B
ASP
25
B
ASP
26
44
1_555
B
GLY
27
B
GLY
28
44
1_555
B
ALA
28
B
ALA
29
44
1_555
B
ASP
29
B
ASP
30
44
1_555
B
ASP
30
B
ASP
31
44
1_555
B
VAL
32
B
VAL
33
44
1_555
B
GLY
48
B
GLY
49
44
1_555
B
GLY
49
B
GLY
50
44
1_555
B
ILE
50
B
ILE
51
44
1_555
B
PRO
81
B
PRO
82
44
1_555
B
VAL
82
B
VAL
83
44
1_555
B
ILE
84
B
ILE
85
44
1_555
B
HOH
210
G
HOH
44
1_555
B
HOH
354
G
HOH
44
1_555
B
HOH
399
G
HOH
44
1_555
B
HOH
429
G
HOH
44
1_555
A
GLN
18
A
GLN
19
12
1_556
A
MET
36
A
MET
37
12
1_556
A
SER
37
A
SER
38
12
1_556
B
THR
12
B
THR
13
12
1_555
B
ILE
13
B
ILE
14
12
1_555
B
LYS
14
B
LYS
15
12
1_555
B
LEU
19
B
LEU
20
12
1_555
B
GLU
65
B
GLU
66
12
1_555
B
ALA
67
B
ALA
68
12
1_555
B
GLY
68
B
GLY
69
12
1_555
B
HOH
232
G
HOH
12
1_555
B
HOH
260
G
HOH
12
1_555
A
HOH
407
F
HOH
8
3_546
B
GLU
35
B
GLU
36
8
1_555
B
LYS
55
B
LYS
56
8
1_555
B
ARG
57
B
ARG
58
8
1_555
B
VAL
77
B
VAL
78
8
1_555
B
GLY
78
B
GLY
79
8
1_555
B
HOH
206
G
HOH
8
1_555
B
HOH
278
G
HOH
8
1_555
18
P 21 21 2