0.017111
0.000000
0.000000
0.000000
0.011330
0.000000
0.000000
0.000000
0.023288
0.00000
0.00000
0.00000
Munshi, S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
58.44
88.26
42.94
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
C3 H7 N O2 S
121.158
y
CYSTEINE
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
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
C36 H47 N5 O4
613.789
N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE
INDINAVIR
non-polymer
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
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
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
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
N
N
75
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
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
N
N
89
S
C
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
N
97
N
O
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
N
N
109
S
C
N
110
N
C
N
111
N
O
N
112
N
C
N
113
N
C
N
114
N
C
N
115
N
O
N
116
N
O
N
117
N
O
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
N
N
128
N
C
N
129
N
C
N
130
N
O
N
131
N
O
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
N
N
138
S
C
N
139
N
C
N
140
N
O
N
141
N
C
Y
142
N
C
Y
143
N
N
Y
144
N
C
Y
145
N
C
Y
146
N
N
N
147
N
O
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
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
O
N
159
N
H
N
160
N
H
N
161
N
N
N
162
S
C
N
163
N
C
N
164
N
O
N
165
S
C
N
166
N
C
N
167
N
C
N
168
N
C
N
169
N
O
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
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
N
N
184
S
C
N
185
N
C
N
186
N
O
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
O
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
N
N
206
S
C
N
207
N
C
N
208
N
O
N
209
N
C
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
N
N
214
N
O
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
N
N
231
S
C
N
232
N
C
N
233
N
O
N
234
N
C
N
235
N
C
N
236
N
S
N
237
N
C
N
238
N
O
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
N
N
251
N
C
N
252
S
C
N
253
N
C
N
254
N
O
N
255
N
N
N
256
N
C
N
257
N
C
N
258
N
C
N
259
N
C
N
260
N
N
N
261
N
C
N
262
N
C
N
263
N
C
N
264
S
C
N
265
N
O
N
266
N
C
N
267
R
C
N
268
N
C
Y
269
N
C
Y
270
N
C
Y
271
N
C
Y
272
N
C
Y
273
N
C
Y
274
N
C
N
275
N
C
N
276
N
O
N
277
N
N
N
278
S
C
N
279
R
C
N
280
N
O
N
281
N
C
Y
282
N
C
Y
283
N
C
Y
284
N
C
Y
285
N
C
Y
286
N
C
Y
287
N
C
N
288
N
C
Y
289
N
C
Y
290
N
C
Y
291
N
N
Y
292
N
C
Y
293
N
C
Y
294
N
C
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
H
N
308
N
H
N
309
N
H
N
310
N
H
N
311
N
H
N
312
N
H
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
H
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
H
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
N
N
343
S
C
N
344
N
C
N
345
N
O
N
346
N
C
Y
347
N
C
Y
348
N
C
Y
349
N
C
Y
350
N
C
Y
351
N
C
Y
352
N
C
N
353
N
O
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
N
N
366
S
C
N
367
N
C
N
368
N
O
N
369
N
C
N
370
N
C
N
371
N
C
N
372
N
O
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
H
N
378
N
H
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
N
N
383
S
C
N
384
N
C
N
385
N
O
N
386
R
C
N
387
N
O
N
388
N
C
N
389
N
O
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
N
N
400
S
C
N
401
N
C
N
402
N
O
N
403
N
C
Y
404
N
C
Y
405
N
C
Y
406
N
C
Y
407
N
N
Y
408
N
C
Y
409
N
C
Y
410
N
C
Y
411
N
C
Y
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
H
N
424
N
H
N
425
N
H
N
426
N
N
N
427
S
C
N
428
N
C
N
429
N
O
N
430
N
C
Y
431
N
C
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
O
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
N
455
N
C
N
456
N
C
N
457
N
O
N
458
N
H
N
459
N
H
N
460
N
H
N
461
N
H
N
462
N
H
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
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
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
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
doub
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
doub
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
doub
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
doub
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
doub
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
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
Y
140
N
sing
Y
141
N
doub
Y
142
N
doub
N
143
N
sing
Y
144
N
sing
N
145
N
sing
Y
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
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
doub
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
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
doub
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
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
sing
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
doub
N
201
N
sing
N
202
N
sing
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
sing
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
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
doub
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
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
doub
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
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
sing
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
Y
285
N
doub
Y
286
N
sing
Y
287
N
sing
N
288
N
sing
Y
289
N
doub
N
290
N
sing
Y
291
N
sing
N
292
N
sing
Y
293
N
doub
N
294
N
sing
N
295
N
sing
N
296
N
doub
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
sing
N
308
N
sing
N
309
N
sing
Y
310
N
doub
Y
311
N
sing
Y
312
N
sing
N
313
N
sing
Y
314
N
doub
N
315
N
sing
Y
316
N
sing
N
317
N
sing
Y
318
N
doub
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
Y
323
N
sing
Y
324
N
doub
Y
325
N
doub
N
326
N
sing
Y
327
N
sing
Y
328
N
doub
N
329
N
sing
Y
330
N
sing
N
331
N
sing
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
doub
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
Y
344
N
doub
Y
345
N
sing
Y
346
N
sing
N
347
N
sing
Y
348
N
doub
N
349
N
sing
Y
350
N
doub
N
351
N
sing
Y
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
doub
N
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
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
doub
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
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
doub
N
396
N
sing
N
397
N
sing
N
398
N
sing
N
399
N
sing
Y
400
N
doub
Y
401
N
sing
Y
402
N
sing
N
403
N
sing
Y
404
N
doub
Y
405
N
sing
Y
406
N
sing
N
407
N
sing
Y
408
N
sing
Y
409
N
doub
N
410
N
sing
Y
411
N
doub
N
412
N
sing
Y
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
sing
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
doub
N
424
N
sing
N
425
N
sing
N
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
doub
N
433
N
sing
Y
434
N
doub
N
435
N
sing
Y
436
N
sing
N
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
N
452
N
sing
N
453
N
sing
N
454
N
sing
N
455
N
sing
N
456
N
sing
N
457
N
sing
N
458
N
sing
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
56
381
388
10.1107/S0907444900000469
10739910
An alternate binding site for the P1-P3 group of a class of potent HIV-1 protease inhibitors as a result of concerted structural change in the 80s loop of the protease.
2000
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
269
26344
26348
Crystal Structure at 1.9-A Resolution of Human Immunodeficiency Virus (HIV) II Protease Complexed with L-735,524, an Orally Bioavailable Inhibitor of the HIV Proteases
1994
10.2210/pdb1c6y/pdb
pdb_00001c6y
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
x-ray
1
1.0
NY5 ISOLATE
10801.674
PROTEIN (PROTEASE)
3.4.24.-
2
man
polymer
613.789
N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE
1
syn
non-polymer
18.015
water
84
nat
water
no
no
PQITLWQRPVVTIKIGGQLMEALIDTGADDTVLEEMDLPGRWKPKIIGGIGGFVKVRQYDQIPIEICGHKVIGTVLVGPT
PTNIIGRNLLTQIGCTLNF
PQITLWQRPVVTIKIGGQLMEALIDTGADDTVLEEMDLPGRWKPKIIGGIGGFVKVRQYDQIPIEICGHKVIGTVLVGPT
PTNIIGRNLLTQIGCTLNF
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
Lentivirus
Escherichia
sample
NY5 ISOLATE
11676
Human immunodeficiency virus 1
562
Escherichia coli
2.56
51.98
THE CRYSTAL WAS PREPARED WITH CO CRYSTALLIZATION METHOD.
9X MUTANT PROTEASE HAS NINE POINT MUTATIONS COMPARED TO
WILD TYPE: L10V,K20M,L24I,S37D,M46I,I54V,L63P,A71V,V82T
THERE IS ONE PROTEASE DIMER IN AN ASYMMETRICAL UNIT. THE
TWO MOLECULES ARE LABELED AS CHAIN A AND CHAIN B. THERE
IS ONE L-735,524 INHIBITOR MOLECULE LABELED AS MK1.
chem_comp_atom
chem_comp_bond
database_2
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2000-12-28
1
1
2008-04-26
1
2
2011-07-13
1
3
2023-12-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
HIV-1 protease with L-739,622
hiv-1 protease with saquinavir
hiv-1 protease with L-756,423
RCSB
Y
RCSB
1999-12-28
REL
MK1
N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE
HOH
water
L-735,524 IS N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-
TERTIARY BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]
-4(S)-HYDROXY-2(R)-PHENYLMETHLPENTANAMIDE.
L73
524
2
MK1
MK1
524
B
HOH
305
3
HOH
HOH
305
A
HOH
309
3
HOH
HOH
309
A
HOH
317
3
HOH
HOH
317
A
HOH
320
3
HOH
HOH
320
A
HOH
321
3
HOH
HOH
321
A
HOH
324
3
HOH
HOH
324
A
HOH
326
3
HOH
HOH
326
A
HOH
327
3
HOH
HOH
327
A
HOH
329
3
HOH
HOH
329
A
HOH
330
3
HOH
HOH
330
A
HOH
333
3
HOH
HOH
333
A
HOH
334
3
HOH
HOH
334
A
HOH
335
3
HOH
HOH
335
A
HOH
336
3
HOH
HOH
336
A
HOH
337
3
HOH
HOH
337
A
HOH
338
3
HOH
HOH
338
A
HOH
339
3
HOH
HOH
339
A
HOH
340
3
HOH
HOH
340
A
HOH
343
3
HOH
HOH
343
A
HOH
344
3
HOH
HOH
344
A
HOH
346
3
HOH
HOH
346
A
HOH
355
3
HOH
HOH
355
A
HOH
358
3
HOH
HOH
358
A
HOH
359
3
HOH
HOH
359
A
HOH
360
3
HOH
HOH
360
A
HOH
361
3
HOH
HOH
361
A
HOH
363
3
HOH
HOH
363
A
HOH
367
3
HOH
HOH
367
A
HOH
373
3
HOH
HOH
373
A
HOH
374
3
HOH
HOH
374
A
HOH
377
3
HOH
HOH
377
A
HOH
379
3
HOH
HOH
379
A
HOH
381
3
HOH
HOH
381
A
HOH
382
3
HOH
HOH
382
A
HOH
383
3
HOH
HOH
383
A
HOH
384
3
HOH
HOH
384
A
HOH
300
3
HOH
HOH
300
B
HOH
301
3
HOH
HOH
301
B
HOH
302
3
HOH
HOH
302
B
HOH
303
3
HOH
HOH
303
B
HOH
304
3
HOH
HOH
304
B
HOH
306
3
HOH
HOH
306
B
HOH
307
3
HOH
HOH
307
B
HOH
308
3
HOH
HOH
308
B
HOH
310
3
HOH
HOH
310
B
HOH
311
3
HOH
HOH
311
B
HOH
312
3
HOH
HOH
312
B
HOH
313
3
HOH
HOH
313
B
HOH
314
3
HOH
HOH
314
B
HOH
315
3
HOH
HOH
315
B
HOH
316
3
HOH
HOH
316
B
HOH
318
3
HOH
HOH
318
B
HOH
319
3
HOH
HOH
319
B
HOH
322
3
HOH
HOH
322
B
HOH
323
3
HOH
HOH
323
B
HOH
325
3
HOH
HOH
325
B
HOH
328
3
HOH
HOH
328
B
HOH
331
3
HOH
HOH
331
B
HOH
332
3
HOH
HOH
332
B
HOH
341
3
HOH
HOH
341
B
HOH
342
3
HOH
HOH
342
B
HOH
345
3
HOH
HOH
345
B
HOH
347
3
HOH
HOH
347
B
HOH
349
3
HOH
HOH
349
B
HOH
350
3
HOH
HOH
350
B
HOH
351
3
HOH
HOH
351
B
HOH
352
3
HOH
HOH
352
B
HOH
353
3
HOH
HOH
353
B
HOH
354
3
HOH
HOH
354
B
HOH
356
3
HOH
HOH
356
B
HOH
357
3
HOH
HOH
357
B
HOH
362
3
HOH
HOH
362
B
HOH
364
3
HOH
HOH
364
B
HOH
365
3
HOH
HOH
365
B
HOH
366
3
HOH
HOH
366
B
HOH
368
3
HOH
HOH
368
B
HOH
369
3
HOH
HOH
369
B
HOH
370
3
HOH
HOH
370
B
HOH
371
3
HOH
HOH
371
B
HOH
372
3
HOH
HOH
372
B
HOH
375
3
HOH
HOH
375
B
HOH
376
3
HOH
HOH
376
B
HOH
378
3
HOH
HOH
378
B
HOH
380
3
HOH
HOH
380
B
PRO
1
n
1
PRO
1
A
GLN
2
n
2
GLN
2
A
ILE
3
n
3
ILE
3
A
THR
4
n
4
THR
4
A
LEU
5
n
5
LEU
5
A
TRP
6
n
6
TRP
6
A
GLN
7
n
7
GLN
7
A
ARG
8
n
8
ARG
8
A
PRO
9
n
9
PRO
9
A
VAL
10
n
10
VAL
10
A
VAL
11
n
11
VAL
11
A
THR
12
n
12
THR
12
A
ILE
13
n
13
ILE
13
A
LYS
14
n
14
LYS
14
A
ILE
15
n
15
ILE
15
A
GLY
16
n
16
GLY
16
A
GLY
17
n
17
GLY
17
A
GLN
18
n
18
GLN
18
A
LEU
19
n
19
LEU
19
A
MET
20
n
20
MET
20
A
GLU
21
n
21
GLU
21
A
ALA
22
n
22
ALA
22
A
LEU
23
n
23
LEU
23
A
ILE
24
n
24
ILE
24
A
ASP
25
n
25
ASP
25
A
THR
26
n
26
THR
26
A
GLY
27
n
27
GLY
27
A
ALA
28
n
28
ALA
28
A
ASP
29
n
29
ASP
29
A
ASP
30
n
30
ASP
30
A
THR
31
n
31
THR
31
A
VAL
32
n
32
VAL
32
A
LEU
33
n
33
LEU
33
A
GLU
34
n
34
GLU
34
A
GLU
35
n
35
GLU
35
A
MET
36
n
36
MET
36
A
ASP
37
n
37
ASP
37
A
LEU
38
n
38
LEU
38
A
PRO
39
n
39
PRO
39
A
GLY
40
n
40
GLY
40
A
ARG
41
n
41
ARG
41
A
TRP
42
n
42
TRP
42
A
LYS
43
n
43
LYS
43
A
PRO
44
n
44
PRO
44
A
LYS
45
n
45
LYS
45
A
ILE
46
n
46
ILE
46
A
ILE
47
n
47
ILE
47
A
GLY
48
n
48
GLY
48
A
GLY
49
n
49
GLY
49
A
ILE
50
n
50
ILE
50
A
GLY
51
n
51
GLY
51
A
GLY
52
n
52
GLY
52
A
PHE
53
n
53
PHE
53
A
VAL
54
n
54
VAL
54
A
LYS
55
n
55
LYS
55
A
VAL
56
n
56
VAL
56
A
ARG
57
n
57
ARG
57
A
GLN
58
n
58
GLN
58
A
TYR
59
n
59
TYR
59
A
ASP
60
n
60
ASP
60
A
GLN
61
n
61
GLN
61
A
ILE
62
n
62
ILE
62
A
PRO
63
n
63
PRO
63
A
ILE
64
n
64
ILE
64
A
GLU
65
n
65
GLU
65
A
ILE
66
n
66
ILE
66
A
CYS
67
n
67
CYS
67
A
GLY
68
n
68
GLY
68
A
HIS
69
n
69
HIS
69
A
LYS
70
n
70
LYS
70
A
VAL
71
n
71
VAL
71
A
ILE
72
n
72
ILE
72
A
GLY
73
n
73
GLY
73
A
THR
74
n
74
THR
74
A
VAL
75
n
75
VAL
75
A
LEU
76
n
76
LEU
76
A
VAL
77
n
77
VAL
77
A
GLY
78
n
78
GLY
78
A
PRO
79
n
79
PRO
79
A
THR
80
n
80
THR
80
A
PRO
81
n
81
PRO
81
A
THR
82
n
82
THR
82
A
ASN
83
n
83
ASN
83
A
ILE
84
n
84
ILE
84
A
ILE
85
n
85
ILE
85
A
GLY
86
n
86
GLY
86
A
ARG
87
n
87
ARG
87
A
ASN
88
n
88
ASN
88
A
LEU
89
n
89
LEU
89
A
LEU
90
n
90
LEU
90
A
THR
91
n
91
THR
91
A
GLN
92
n
92
GLN
92
A
ILE
93
n
93
ILE
93
A
GLY
94
n
94
GLY
94
A
CYS
95
n
95
CYS
95
A
THR
96
n
96
THR
96
A
LEU
97
n
97
LEU
97
A
ASN
98
n
98
ASN
98
A
PHE
99
n
99
PHE
99
A
PRO
201
n
1
PRO
201
B
GLN
202
n
2
GLN
202
B
ILE
203
n
3
ILE
203
B
THR
204
n
4
THR
204
B
LEU
205
n
5
LEU
205
B
TRP
206
n
6
TRP
206
B
GLN
207
n
7
GLN
207
B
ARG
208
n
8
ARG
208
B
PRO
209
n
9
PRO
209
B
VAL
210
n
10
VAL
210
B
VAL
211
n
11
VAL
211
B
THR
212
n
12
THR
212
B
ILE
213
n
13
ILE
213
B
LYS
214
n
14
LYS
214
B
ILE
215
n
15
ILE
215
B
GLY
216
n
16
GLY
216
B
GLY
217
n
17
GLY
217
B
GLN
218
n
18
GLN
218
B
LEU
219
n
19
LEU
219
B
MET
220
n
20
MET
220
B
GLU
221
n
21
GLU
221
B
ALA
222
n
22
ALA
222
B
LEU
223
n
23
LEU
223
B
ILE
224
n
24
ILE
224
B
ASP
225
n
25
ASP
225
B
THR
226
n
26
THR
226
B
GLY
227
n
27
GLY
227
B
ALA
228
n
28
ALA
228
B
ASP
229
n
29
ASP
229
B
ASP
230
n
30
ASP
230
B
THR
231
n
31
THR
231
B
VAL
232
n
32
VAL
232
B
LEU
233
n
33
LEU
233
B
GLU
234
n
34
GLU
234
B
GLU
235
n
35
GLU
235
B
MET
236
n
36
MET
236
B
ASP
237
n
37
ASP
237
B
LEU
238
n
38
LEU
238
B
PRO
239
n
39
PRO
239
B
GLY
240
n
40
GLY
240
B
ARG
241
n
41
ARG
241
B
TRP
242
n
42
TRP
242
B
LYS
243
n
43
LYS
243
B
PRO
244
n
44
PRO
244
B
LYS
245
n
45
LYS
245
B
ILE
246
n
46
ILE
246
B
ILE
247
n
47
ILE
247
B
GLY
248
n
48
GLY
248
B
GLY
249
n
49
GLY
249
B
ILE
250
n
50
ILE
250
B
GLY
251
n
51
GLY
251
B
GLY
252
n
52
GLY
252
B
PHE
253
n
53
PHE
253
B
VAL
254
n
54
VAL
254
B
LYS
255
n
55
LYS
255
B
VAL
256
n
56
VAL
256
B
ARG
257
n
57
ARG
257
B
GLN
258
n
58
GLN
258
B
TYR
259
n
59
TYR
259
B
ASP
260
n
60
ASP
260
B
GLN
261
n
61
GLN
261
B
ILE
262
n
62
ILE
262
B
PRO
263
n
63
PRO
263
B
ILE
264
n
64
ILE
264
B
GLU
265
n
65
GLU
265
B
ILE
266
n
66
ILE
266
B
CYS
267
n
67
CYS
267
B
GLY
268
n
68
GLY
268
B
HIS
269
n
69
HIS
269
B
LYS
270
n
70
LYS
270
B
VAL
271
n
71
VAL
271
B
ILE
272
n
72
ILE
272
B
GLY
273
n
73
GLY
273
B
THR
274
n
74
THR
274
B
VAL
275
n
75
VAL
275
B
LEU
276
n
76
LEU
276
B
VAL
277
n
77
VAL
277
B
GLY
278
n
78
GLY
278
B
PRO
279
n
79
PRO
279
B
THR
280
n
80
THR
280
B
PRO
281
n
81
PRO
281
B
THR
282
n
82
THR
282
B
ASN
283
n
83
ASN
283
B
ILE
284
n
84
ILE
284
B
ILE
285
n
85
ILE
285
B
GLY
286
n
86
GLY
286
B
ARG
287
n
87
ARG
287
B
ASN
288
n
88
ASN
288
B
LEU
289
n
89
LEU
289
B
LEU
290
n
90
LEU
290
B
THR
291
n
91
THR
291
B
GLN
292
n
92
GLN
292
B
ILE
293
n
93
ILE
293
B
GLY
294
n
94
GLY
294
B
CYS
295
n
95
CYS
295
B
THR
296
n
96
THR
296
B
LEU
297
n
97
LEU
297
B
ASN
298
n
98
ASN
298
B
PHE
299
n
99
PHE
299
B
author_and_software_defined_assembly
PISA
2
dimeric
5060
-21
9560
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
3
B
O
LEU
297
B
O
LEU
97
B
N
ASN
298
B
N
ASN
98
A
O
THR
96
A
O
THR
96
A
O
LEU
97
A
O
LEU
97
B
N
ILE
203
B
N
ILE
3
A
N
GLY
49
A
N
GLY
49
A
O
GLY
52
A
O
GLY
52
A
N
ILE
66
A
N
ILE
66
A
O
HIS
69
A
O
HIS
69
A
N
LEU
76
A
N
LEU
76
A
O
THR
31
A
O
THR
31
A
O
VAL
32
A
O
VAL
32
A
N
ILE
84
A
N
ILE
84
A
N
ILE
85
A
N
ILE
85
A
O
LEU
23
A
O
LEU
23
A
O
ALA
22
A
O
ALA
22
A
N
VAL
11
A
N
VAL
11
A
O
LYS
14
A
O
LYS
14
A
N
GLU
65
A
N
GLU
65
B
O
ILE
247
B
O
ILE
47
B
N
VAL
254
B
N
VAL
54
B
O
ILE
266
B
O
ILE
66
B
N
HIS
269
B
N
HIS
69
B
O
LEU
276
B
O
LEU
76
B
N
LEU
233
B
N
LEU
33
B
O
VAL
232
B
O
VAL
32
B
N
ILE
284
B
N
ILE
84
B
N
ASN
283
B
N
ASN
83
B
O
GLU
221
B
O
GLU
21
B
O
ALA
222
B
O
ALA
22
B
N
VAL
211
B
N
VAL
11
B
N
LYS
214
B
N
LYS
14
B
O
GLU
265
B
O
GLU
65
1
-9.04
1.40
111.50
102.46
A
A
A
CA
N
CD
PRO
PRO
PRO
1
1
1
N
1
-9.62
1.40
111.50
101.88
B
B
B
CA
N
CD
PRO
PRO
PRO
201
201
201
N
1
A
PRO
9
-67.63
93.58
1
A
GLU
34
-69.49
-175.73
1
A
GLN
61
34.98
56.83
1
A
PRO
79
-66.28
82.99
1
B
PRO
209
-66.48
97.40
1
B
CYS
267
39.45
60.37
0.3100000
0.1800000
0.1800000
2.5
8.0
1
2.0
2.5
8.0
84
1643
45
0
1514
0.017
2.1
1C6Y
35099
7254
0.0520000
1
89.0
2.5
2.59
84.0
refinement
X-PLOR
ALTERNATE BINDING SITE FOR THE P1-P3 GROUP OF A CLASS OF POTENT HIV-1 PROTEASE INHIBITORS AS A RESULT OF CONCERTED STRUCTURAL CHANGE IN 80'S LOOP.
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
A
GLY
86
A
GLY
86
HELX_P
A
THR
91
A
THR
91
1
1
6
A
GLN
92
A
GLN
92
HELX_P
A
GLY
94
A
GLY
94
5
2
3
B
GLY
286
B
GLY
86
HELX_P
B
THR
291
B
THR
91
1
3
6
HYDROLASE
hydrolase
O09893_9HIV1
UNP
1
O09893
1
99
1C6Y
1
99
O09893
A
1
1
99
1
99
1C6Y
201
299
O09893
B
1
1
99
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
2
A
THR
4
A
THR
4
B
THR
296
B
THR
96
B
ASN
298
B
ASN
98
A
THR
96
A
THR
96
A
ASN
98
A
ASN
98
B
GLN
202
B
GLN
2
B
ILE
203
B
ILE
3
A
LYS
43
A
LYS
43
A
GLY
49
A
GLY
49
A
GLY
52
A
GLY
52
A
ILE
66
A
ILE
66
A
HIS
69
A
HIS
69
A
VAL
77
A
VAL
77
A
THR
31
A
THR
31
A
LEU
33
A
LEU
33
A
ILE
84
A
ILE
84
A
ILE
85
A
ILE
85
A
GLN
18
A
GLN
18
A
ILE
24
A
ILE
24
A
VAL
10
A
VAL
10
A
ILE
15
A
ILE
15
A
GLY
52
A
GLY
52
A
ILE
66
A
ILE
66
B
TRP
242
B
TRP
42
B
GLY
248
B
GLY
48
B
PHE
253
B
PHE
53
B
ILE
266
B
ILE
66
B
HIS
269
B
HIS
69
B
GLY
278
B
GLY
78
B
VAL
232
B
VAL
32
B
GLU
234
B
GLU
34
B
ASN
283
B
ASN
83
B
ILE
285
B
ILE
85
B
GLN
218
B
GLN
18
B
ILE
224
B
ILE
24
B
VAL
210
B
VAL
10
B
ILE
215
B
ILE
15
B
PHE
253
B
PHE
53
B
ILE
266
B
ILE
66
BINDING SITE FOR RESIDUE MK1 B 524
B
MK1
524
Software
20
A
ASP
25
A
ASP
25
20
1_555
A
GLY
48
A
GLY
48
20
1_555
A
GLY
49
A
GLY
49
20
1_555
A
THR
82
A
THR
82
20
1_555
A
ILE
84
A
ILE
84
20
1_555
B
ASP
225
B
ASP
25
20
1_555
B
GLY
227
B
GLY
27
20
1_555
B
ALA
228
B
ALA
28
20
1_555
B
ASP
229
B
ASP
29
20
1_555
B
ASP
230
B
ASP
30
20
1_555
B
GLY
248
B
GLY
48
20
1_555
B
GLY
249
B
GLY
49
20
1_555
B
ILE
250
B
ILE
50
20
1_555
B
THR
280
B
THR
80
20
1_555
B
PRO
281
B
PRO
81
20
1_555
B
THR
282
B
THR
82
20
1_555
B
ILE
284
B
ILE
84
20
1_555
B
HOH
302
E
HOH
20
1_555
B
HOH
311
E
HOH
20
1_555
B
HOH
328
E
HOH
20
1_555
18
P 21 21 2