0.019493
0.000000
0.000000
0.000000
0.017007
0.000000
0.000000
0.000000
0.016051
0.00000
0.00000
0.00000
Martin, J.L.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
51.300
58.800
62.300
C4 H9 N O2
103.120
n
ALPHA-AMINOBUTYRIC ACID
L-peptide linking
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
H2 N
16.023
AMINO GROUP
non-polymer
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C14 H20 Br N O4
346.217
4-{4-[(2S,3R)-2-amino-4-bromo-3-hydroxybutyl]phenoxy}butanoic acid
non-polymer
O4 S -2
96.063
SULFATE ION
non-polymer
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
C
N
7
N
O
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
H
N
15
N
H
N
16
N
H
N
17
N
N
N
18
S
C
N
19
N
C
N
20
N
O
N
21
N
C
N
22
N
O
N
23
N
H
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
N
N
31
S
C
N
32
N
C
N
33
N
O
N
34
N
C
N
35
N
C
N
36
N
C
N
37
N
N
N
38
N
C
N
39
N
N
N
40
N
N
N
41
N
O
N
42
N
H
N
43
N
H
N
44
N
H
N
45
N
H
N
46
N
H
N
47
N
H
N
48
N
H
N
49
N
H
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
N
N
58
S
C
N
59
N
C
N
60
N
O
N
61
N
C
N
62
N
C
N
63
N
O
N
64
N
N
N
65
N
O
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
N
N
75
S
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
C
N
80
N
O
N
81
N
O
N
82
N
O
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
N
N
91
R
C
N
92
N
C
N
93
N
O
N
94
N
C
N
95
N
S
N
96
N
O
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
H
N
104
N
N
N
105
S
C
N
106
N
C
N
107
N
O
N
108
N
C
N
109
N
C
N
110
N
C
N
111
N
O
N
112
N
N
N
113
N
O
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
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
N
N
125
S
C
N
126
N
C
N
127
N
O
N
128
N
C
N
129
N
C
N
130
N
C
N
131
N
O
N
132
N
O
N
133
N
O
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
N
C
N
145
N
C
N
146
N
O
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
N
N
154
S
C
N
155
N
C
N
156
N
O
N
157
N
C
Y
158
N
C
Y
159
N
N
Y
160
N
C
Y
161
N
C
Y
162
N
N
N
163
N
O
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
O
N
175
N
H
N
176
N
H
N
177
N
N
N
178
S
C
N
179
N
C
N
180
N
O
N
181
S
C
N
182
N
C
N
183
N
C
N
184
N
C
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
H
N
197
N
H
N
198
N
H
N
199
N
N
N
200
S
C
N
201
N
C
N
202
N
O
N
203
N
C
N
204
N
C
N
205
N
C
N
206
N
C
N
207
N
O
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
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
N
N
222
S
C
N
223
N
C
N
224
N
O
N
225
N
C
N
226
N
C
N
227
N
C
N
228
N
C
N
229
N
N
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
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
N
N
247
S
C
N
248
N
C
N
249
N
O
N
250
N
C
N
251
N
C
N
252
N
S
N
253
N
C
N
254
N
O
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
H
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
N
N
267
N
H
N
268
N
H
N
269
N
N
N
270
S
C
N
271
N
C
N
272
N
O
N
273
N
C
Y
274
N
C
Y
275
N
C
Y
276
N
C
Y
277
N
C
Y
278
N
C
Y
279
N
C
N
280
N
O
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
H
N
292
N
N
N
293
S
C
N
294
N
C
N
295
N
O
N
296
N
C
N
297
N
C
N
298
N
C
N
299
N
O
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
R
C
N
310
N
N
N
311
N
O
N
312
N
C
N
313
N
O
N
314
N
C
N
315
N
C
N
316
N
C
N
317
N
C
N
318
S
C
N
319
N
C
Y
320
N
C
N
321
N
O
Y
322
N
C
Y
323
N
C
Y
324
N
C
Y
325
N
C
Y
326
N
C
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
O
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
BR
N
339
N
H
N
340
N
H
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
S
N
350
N
O
N
351
N
O
N
352
N
O
N
353
N
O
N
354
N
N
N
355
S
C
N
356
N
C
N
357
N
O
N
358
R
C
N
359
N
O
N
360
N
C
N
361
N
O
N
362
N
H
N
363
N
H
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
N
N
372
S
C
N
373
N
C
N
374
N
O
N
375
N
C
Y
376
N
C
Y
377
N
C
Y
378
N
C
Y
379
N
N
Y
380
N
C
Y
381
N
C
Y
382
N
C
Y
383
N
C
Y
384
N
C
N
385
N
O
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
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
N
N
399
S
C
N
400
N
C
N
401
N
O
N
402
N
C
Y
403
N
C
Y
404
N
C
Y
405
N
C
Y
406
N
C
Y
407
N
C
Y
408
N
C
N
409
N
O
N
410
N
O
N
411
N
H
N
412
N
H
N
413
N
H
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
N
N
423
S
C
N
424
N
C
N
425
N
O
N
426
N
C
N
427
N
C
N
428
N
C
N
429
N
O
N
430
N
H
N
431
N
H
N
432
N
H
N
433
N
H
N
434
N
H
N
435
N
H
N
436
N
H
N
437
N
H
N
438
N
H
N
439
N
H
N
440
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
sing
N
20
N
sing
N
21
N
sing
N
22
N
doub
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
sing
N
34
N
doub
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
sing
N
46
N
sing
N
47
N
sing
N
48
N
doub
N
49
N
sing
N
50
N
sing
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
doub
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
doub
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
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
doub
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
doub
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
doub
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
doub
N
113
N
sing
N
114
N
sing
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
doub
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
doub
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
sing
N
141
N
doub
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
doub
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
Y
155
N
sing
Y
156
N
doub
Y
157
N
doub
N
158
N
sing
Y
159
N
sing
N
160
N
sing
Y
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
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
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
doub
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
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
doub
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
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
doub
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
sing
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
doub
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
Y
265
N
doub
Y
266
N
sing
Y
267
N
sing
N
268
N
sing
Y
269
N
doub
N
270
N
sing
Y
271
N
doub
N
272
N
sing
Y
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
doub
N
284
N
sing
N
285
N
sing
N
286
N
sing
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
doub
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
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
Y
321
N
sing
N
322
N
sing
N
323
N
sing
Y
324
N
sing
Y
325
N
doub
N
326
N
sing
N
327
N
sing
Y
328
N
doub
Y
329
N
sing
N
330
N
sing
Y
331
N
doub
N
332
N
sing
N
333
N
sing
N
334
N
doub
N
335
N
doub
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
doub
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
sing
N
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
doub
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
Y
365
N
doub
Y
366
N
sing
Y
367
N
sing
N
368
N
sing
Y
369
N
doub
Y
370
N
sing
Y
371
N
sing
N
372
N
sing
Y
373
N
sing
Y
374
N
doub
N
375
N
sing
Y
376
N
doub
N
377
N
sing
Y
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
doub
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
Y
393
N
doub
Y
394
N
sing
Y
395
N
sing
N
396
N
sing
Y
397
N
doub
N
398
N
sing
Y
399
N
doub
N
400
N
sing
Y
401
N
sing
N
402
N
sing
N
403
N
sing
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
doub
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
sing
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
sing
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
117
10220
10226
-1
REGIOSELECTIVE STRUCTURAL AND FUNCTIONAL MIMICRY OF PEPTIDES - DESIGN OF HYDROLYTICALLY-STABLE CYCLIC PEPTIDOMIMETIC INHIBITORS OF HIV-1 PROTEASE.
1995
10.2210/pdb1cpi/pdb
pdb_00001cpi
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
289
1
IMAGE PLATE
1993-12-10
RIGAKU
GRAPHITE
M
x-ray
1
1.5418
1.0
1.5418
10764.636
HIV-1 PROTEASE
2
syn
polymer
767.731
CYCLIC PEPTIDE INHIBITOR
1
syn
polymer
96.063
SULFATE ION
3
syn
non-polymer
18.015
water
95
nat
water
HIV-1 PR
no
yes
PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEI(ABA)GHKAIGTVL
VGPTPVNIIGRNLLTQIG(ABA)TLNF
PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEIAGHKAIGTVLVGPT
PVNIIGRNLLTQIGATLNF
A,B
polypeptide(L)
no
yes
N(RTY)PIV(NH2)
NXPIVX
C
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
n
n
n
n
n
2.12
41.94
5.5
pH 5.5
chem_comp_atom
chem_comp_bond
database_2
pdbx_database_status
pdbx_validate_polymer_linkage
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Atomic model
Database references
Derived calculations
Non-polymer description
Structure summary
Version format compliance
Other
Advisory
Data collection
Database references
Derived calculations
Other
1
0
1996-03-08
1
1
2008-05-22
1
2
2011-07-13
1
3
2012-12-12
1
4
2024-06-05
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Y
BNL
1995-10-16
REL
SO4
SULFATE ION
HOH
water
CHEMICALLY SYNTHESIZED PROTEIN CORRESPONDING TO THE PROTEASE FROM THE HIV-I
sample
Inhibitor
1-{(2R)-2-[(8R,11S)-8-(2-amino-2-oxoethyl)-6,9-dioxo-2-oxa-7,10-diazabicyclo[11.2.2]heptadeca-1(15),13,16-trien-11-yl]-2-hydroxyethyl}-L-prolyl-L-isoleucyl-L-valinamide
Peptide-like
SO4
502
3
SO4
SO4
502
A
SO4
503
3
SO4
SO4
503
A
SO4
501
3
SO4
SO4
501
B
HOH
302
4
HOH
HOH
302
A
HOH
303
4
HOH
HOH
303
A
HOH
304
4
HOH
HOH
304
A
HOH
305
4
HOH
HOH
305
A
HOH
306
4
HOH
HOH
306
A
HOH
307
4
HOH
HOH
307
A
HOH
308
4
HOH
HOH
308
A
HOH
309
4
HOH
HOH
309
A
HOH
310
4
HOH
HOH
310
A
HOH
311
4
HOH
HOH
311
A
HOH
312
4
HOH
HOH
312
A
HOH
313
4
HOH
HOH
313
A
HOH
314
4
HOH
HOH
314
A
HOH
315
4
HOH
HOH
315
A
HOH
316
4
HOH
HOH
316
A
HOH
317
4
HOH
HOH
317
A
HOH
318
4
HOH
HOH
318
A
HOH
331
4
HOH
HOH
331
A
HOH
332
4
HOH
HOH
332
A
HOH
333
4
HOH
HOH
333
A
HOH
334
4
HOH
HOH
334
A
HOH
335
4
HOH
HOH
335
A
HOH
336
4
HOH
HOH
336
A
HOH
337
4
HOH
HOH
337
A
HOH
338
4
HOH
HOH
338
A
HOH
339
4
HOH
HOH
339
A
HOH
340
4
HOH
HOH
340
A
HOH
341
4
HOH
HOH
341
A
HOH
346
4
HOH
HOH
346
A
HOH
347
4
HOH
HOH
347
A
HOH
351
4
HOH
HOH
351
A
HOH
352
4
HOH
HOH
352
A
HOH
353
4
HOH
HOH
353
A
HOH
354
4
HOH
HOH
354
A
HOH
355
4
HOH
HOH
355
A
HOH
356
4
HOH
HOH
356
A
HOH
357
4
HOH
HOH
357
A
HOH
362
4
HOH
HOH
362
A
HOH
363
4
HOH
HOH
363
A
HOH
364
4
HOH
HOH
364
A
HOH
367
4
HOH
HOH
367
A
HOH
369
4
HOH
HOH
369
A
HOH
370
4
HOH
HOH
370
A
HOH
372
4
HOH
HOH
372
A
HOH
373
4
HOH
HOH
373
A
HOH
374
4
HOH
HOH
374
A
HOH
377
4
HOH
HOH
377
A
HOH
378
4
HOH
HOH
378
A
HOH
379
4
HOH
HOH
379
A
HOH
380
4
HOH
HOH
380
A
HOH
385
4
HOH
HOH
385
A
HOH
387
4
HOH
HOH
387
A
HOH
388
4
HOH
HOH
388
A
HOH
389
4
HOH
HOH
389
A
HOH
390
4
HOH
HOH
390
A
HOH
393
4
HOH
HOH
393
A
HOH
394
4
HOH
HOH
394
A
HOH
319
4
HOH
HOH
319
B
HOH
320
4
HOH
HOH
320
B
HOH
321
4
HOH
HOH
321
B
HOH
322
4
HOH
HOH
322
B
HOH
323
4
HOH
HOH
323
B
HOH
324
4
HOH
HOH
324
B
HOH
325
4
HOH
HOH
325
B
HOH
326
4
HOH
HOH
326
B
HOH
327
4
HOH
HOH
327
B
HOH
328
4
HOH
HOH
328
B
HOH
329
4
HOH
HOH
329
B
HOH
330
4
HOH
HOH
330
B
HOH
342
4
HOH
HOH
342
B
HOH
343
4
HOH
HOH
343
B
HOH
344
4
HOH
HOH
344
B
HOH
345
4
HOH
HOH
345
B
HOH
348
4
HOH
HOH
348
B
HOH
349
4
HOH
HOH
349
B
HOH
350
4
HOH
HOH
350
B
HOH
358
4
HOH
HOH
358
B
HOH
359
4
HOH
HOH
359
B
HOH
360
4
HOH
HOH
360
B
HOH
361
4
HOH
HOH
361
B
HOH
365
4
HOH
HOH
365
B
HOH
366
4
HOH
HOH
366
B
HOH
368
4
HOH
HOH
368
B
HOH
371
4
HOH
HOH
371
B
HOH
375
4
HOH
HOH
375
B
HOH
376
4
HOH
HOH
376
B
HOH
381
4
HOH
HOH
381
B
HOH
382
4
HOH
HOH
382
B
HOH
383
4
HOH
HOH
383
B
HOH
384
4
HOH
HOH
384
B
HOH
386
4
HOH
HOH
386
B
HOH
391
4
HOH
HOH
391
B
HOH
392
4
HOH
HOH
392
B
HOH
395
4
HOH
HOH
395
B
HOH
301
4
HOH
HOH
301
C
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
LEU
10
n
10
LEU
10
A
VAL
11
n
11
VAL
11
A
THR
12
n
12
THR
12
A
ILE
13
n
13
ILE
13
A
ARG
14
n
14
ARG
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
LYS
20
n
20
LYS
20
A
GLU
21
n
21
GLU
21
A
ALA
22
n
22
ALA
22
A
LEU
23
n
23
LEU
23
A
LEU
24
n
24
LEU
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
ASN
37
n
37
ASN
37
A
LEU
38
n
38
LEU
38
A
PRO
39
n
39
PRO
39
A
GLY
40
n
40
GLY
40
A
LYS
41
n
41
LYS
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
MET
46
n
46
MET
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
ILE
54
n
54
ILE
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
VAL
64
n
64
VAL
64
A
GLU
65
n
65
GLU
65
A
ILE
66
n
66
ILE
66
A
ABA
67
n
67
ABA
67
A
GLY
68
n
68
GLY
68
A
HIS
69
n
69
HIS
69
A
LYS
70
n
70
LYS
70
A
ALA
71
n
71
ALA
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
VAL
82
n
82
VAL
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
ABA
95
n
95
ABA
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
1
n
1
PRO
1
B
GLN
2
n
2
GLN
2
B
ILE
3
n
3
ILE
3
B
THR
4
n
4
THR
4
B
LEU
5
n
5
LEU
5
B
TRP
6
n
6
TRP
6
B
GLN
7
n
7
GLN
7
B
ARG
8
n
8
ARG
8
B
PRO
9
n
9
PRO
9
B
LEU
10
n
10
LEU
10
B
VAL
11
n
11
VAL
11
B
THR
12
n
12
THR
12
B
ILE
13
n
13
ILE
13
B
ARG
14
n
14
ARG
14
B
ILE
15
n
15
ILE
15
B
GLY
16
n
16
GLY
16
B
GLY
17
n
17
GLY
17
B
GLN
18
n
18
GLN
18
B
LEU
19
n
19
LEU
19
B
LYS
20
n
20
LYS
20
B
GLU
21
n
21
GLU
21
B
ALA
22
n
22
ALA
22
B
LEU
23
n
23
LEU
23
B
LEU
24
n
24
LEU
24
B
ASP
25
n
25
ASP
25
B
THR
26
n
26
THR
26
B
GLY
27
n
27
GLY
27
B
ALA
28
n
28
ALA
28
B
ASP
29
n
29
ASP
29
B
ASP
30
n
30
ASP
30
B
THR
31
n
31
THR
31
B
VAL
32
n
32
VAL
32
B
LEU
33
n
33
LEU
33
B
GLU
34
n
34
GLU
34
B
GLU
35
n
35
GLU
35
B
MET
36
n
36
MET
36
B
ASN
37
n
37
ASN
37
B
LEU
38
n
38
LEU
38
B
PRO
39
n
39
PRO
39
B
GLY
40
n
40
GLY
40
B
LYS
41
n
41
LYS
41
B
TRP
42
n
42
TRP
42
B
LYS
43
n
43
LYS
43
B
PRO
44
n
44
PRO
44
B
LYS
45
n
45
LYS
45
B
MET
46
n
46
MET
46
B
ILE
47
n
47
ILE
47
B
GLY
48
n
48
GLY
48
B
GLY
49
n
49
GLY
49
B
ILE
50
n
50
ILE
50
B
GLY
51
n
51
GLY
51
B
GLY
52
n
52
GLY
52
B
PHE
53
n
53
PHE
53
B
ILE
54
n
54
ILE
54
B
LYS
55
n
55
LYS
55
B
VAL
56
n
56
VAL
56
B
ARG
57
n
57
ARG
57
B
GLN
58
n
58
GLN
58
B
TYR
59
n
59
TYR
59
B
ASP
60
n
60
ASP
60
B
GLN
61
n
61
GLN
61
B
ILE
62
n
62
ILE
62
B
PRO
63
n
63
PRO
63
B
VAL
64
n
64
VAL
64
B
GLU
65
n
65
GLU
65
B
ILE
66
n
66
ILE
66
B
ABA
67
n
67
ABA
67
B
GLY
68
n
68
GLY
68
B
HIS
69
n
69
HIS
69
B
LYS
70
n
70
LYS
70
B
ALA
71
n
71
ALA
71
B
ILE
72
n
72
ILE
72
B
GLY
73
n
73
GLY
73
B
THR
74
n
74
THR
74
B
VAL
75
n
75
VAL
75
B
LEU
76
n
76
LEU
76
B
VAL
77
n
77
VAL
77
B
GLY
78
n
78
GLY
78
B
PRO
79
n
79
PRO
79
B
THR
80
n
80
THR
80
B
PRO
81
n
81
PRO
81
B
VAL
82
n
82
VAL
82
B
ASN
83
n
83
ASN
83
B
ILE
84
n
84
ILE
84
B
ILE
85
n
85
ILE
85
B
GLY
86
n
86
GLY
86
B
ARG
87
n
87
ARG
87
B
ASN
88
n
88
ASN
88
B
LEU
89
n
89
LEU
89
B
LEU
90
n
90
LEU
90
B
THR
91
n
91
THR
91
B
GLN
92
n
92
GLN
92
B
ILE
93
n
93
ILE
93
B
GLY
94
n
94
GLY
94
B
ABA
95
n
95
ABA
95
B
THR
96
n
96
THR
96
B
LEU
97
n
97
LEU
97
B
ASN
98
n
98
ASN
98
B
PHE
99
n
99
PHE
99
B
ASN
1
n
1
ASN
1
C
RTY
2
n
2
RTY
2
C
PRO
3
n
3
PRO
3
C
ILE
4
n
4
ILE
4
C
VAL
5
n
5
VAL
5
C
NH2
6
n
6
NH2
6
C
author_and_software_defined_assembly
PISA
3
trimeric
5700
-56
8990
A
ABA
67
ALPHA-AMINOBUTYRIC ACID
A
ABA
67
ALA
A
ABA
95
ALPHA-AMINOBUTYRIC ACID
A
ABA
95
ALA
B
ABA
67
ALPHA-AMINOBUTYRIC ACID
B
ABA
67
ALA
B
ABA
95
ALPHA-AMINOBUTYRIC ACID
B
ABA
95
ALA
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
1
A
CG
LYS
41
A
CG
LYS
41
1
Y
1
A
CD
LYS
41
A
CD
LYS
41
1
Y
1
A
CE
LYS
41
A
CE
LYS
41
1
Y
1
A
NZ
LYS
41
A
NZ
LYS
41
1
Y
1
A
CG
LYS
43
A
CG
LYS
43
1
Y
1
A
CD
LYS
43
A
CD
LYS
43
1
Y
1
A
CE
LYS
43
A
CE
LYS
43
1
Y
1
A
NZ
LYS
43
A
NZ
LYS
43
1
Y
1
A
CG
LYS
45
A
CG
LYS
45
1
Y
1
A
CD
LYS
45
A
CD
LYS
45
1
Y
1
A
CE
LYS
45
A
CE
LYS
45
1
Y
1
A
NZ
LYS
45
A
NZ
LYS
45
1
Y
1
A
CG
LYS
70
A
CG
LYS
70
1
Y
1
A
CD
LYS
70
A
CD
LYS
70
1
Y
1
A
CE
LYS
70
A
CE
LYS
70
1
Y
1
A
NZ
LYS
70
A
NZ
LYS
70
1
Y
1
B
CG
LYS
41
B
CG
LYS
41
1
Y
1
B
CD
LYS
41
B
CD
LYS
41
1
Y
1
B
CE
LYS
41
B
CE
LYS
41
1
Y
1
B
NZ
LYS
41
B
NZ
LYS
41
1
Y
1
B
CG
LYS
43
B
CG
LYS
43
1
Y
1
B
CD
LYS
43
B
CD
LYS
43
1
Y
1
B
CE
LYS
43
B
CE
LYS
43
1
Y
1
B
NZ
LYS
43
B
NZ
LYS
43
1
Y
1
A
PRO
79
-69.91
85.63
1
B
GLU
35
-29.36
119.38
20.9
0.237
0.163
0.163
2.05
8.0
11271
10.00
94.
1
2.0
0.2
2.05
8.0
95
1651
15
0
1541
0.009
1.59
26.9
1.42
1.5
2.0
2.0
2.5
2.05
51.0
1CPI
11539
1.
0.071
1
3.0
94.
model building
X-PLOR
3.1
refinement
X-PLOR
3.1
data reduction
PROCESS
(HIGASHI/RIGAKU)
phasing
X-PLOR
3.1
REGIOSELECTIVE STRUCTURAL AND FUNCTIONAL MIMICRY OF PEPTIDES. DESIGN OF HYDROLYTICALLY STABLE CYCLIC PEPTIDOMIMETIC INHIBITORS OF HIV-1 PROTEASE
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
3
N
N
4
N
N
4
N
N
4
N
N
A
GLY
86
A
GLY
86
HELX_P
A
GLY
94
A
GLY
94
1
HA
9
B
GLY
86
B
GLY
86
HELX_P
B
GLY
94
B
GLY
94
1
HB
9
covale
1.334
both
A
ILE
66
A
C
ILE
66
1_555
A
ABA
67
A
N
ABA
67
1_555
covale
1.325
both
A
ABA
67
A
C
ABA
67
1_555
A
GLY
68
A
N
GLY
68
1_555
covale
1.329
both
A
GLY
94
A
C
GLY
94
1_555
A
ABA
95
A
N
ABA
95
1_555
covale
1.336
both
A
ABA
95
A
C
ABA
95
1_555
A
THR
96
A
N
THR
96
1_555
covale
1.333
both
B
ILE
66
B
C
ILE
66
1_555
B
ABA
67
B
N
ABA
67
1_555
covale
1.329
both
B
ABA
67
B
C
ABA
67
1_555
B
GLY
68
B
N
GLY
68
1_555
covale
1.329
both
B
GLY
94
B
C
GLY
94
1_555
B
ABA
95
B
N
ABA
95
1_555
covale
1.329
both
B
ABA
95
B
C
ABA
95
1_555
B
THR
96
B
N
THR
96
1_555
covale
1.330
both
C
ASN
1
C
N
ASN
1
1_555
C
RTY
2
C
C2
RTY
2
1_555
covale
1.468
both
C
RTY
2
C
C6
RTY
2
1_555
C
PRO
3
C
N
PRO
3
1_555
HYDROLASE/HYDROLASE INHIBITOR
HYDROLASE-HYDROLASE INHIBITOR complex
POL_HV1A2
UNP
1
1
P03369
FFREDLAFLQGKAREFSSEQTRANSPTRRELQVWGGENNSLSEAGADRQGTVSFNFPQITLWQRPLVTIRIGGQLKEALL
DTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNFPISPI
ETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQ
DFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDKDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMT
KILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGFTTPDKKHQKEPPFLWMGYELHPDKWTVQPIM
LPEKDSWTVNDIQKLVGKLNWASQIYAGIKVKQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHEVYYDPSKDL
VAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKVSTESIVIWGKIPKFKLPIQKETWEAWWMEY
WQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTDRGRQKVVSIADTTNQKTELQAIHLA
LQDSGLEVNIVTDSQYALGIIQAQPDKSESELVSQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKVLFLNGI
DKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVDCSPGIWQLDCTHLEGKIILVAVHVASGYIE
AEVIPAETGQETAYFLLKLAGRWPVKTIHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVVESMNNELKKIIGQV
RDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQTKELQKQITKIQNFRVYYRDNKDPLWKGPAKLLWKG
EGAVVIQDNSDIKVVPRRKAKIIRDYGKQMAGDDCVASRQDED
1CPI
PDB
2
1
1CPI
NXPIVX
57
155
1CPI
1
99
P03369
A
1
1
99
57
155
1CPI
1
99
P03369
B
1
1
99
1
6
1CPI
1
6
1CPI
C
2
1
6
1
CYS
conflict
ABA
67
1CPI
A
P03369
UNP
123
67
1
CYS
conflict
ABA
95
1CPI
A
P03369
UNP
151
95
2
CYS
conflict
ABA
67
1CPI
B
P03369
UNP
123
67
2
CYS
conflict
ABA
95
1CPI
B
P03369
UNP
151
95
8
8
4
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
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
GLY
78
A
GLY
78
A
THR
31
A
THR
31
A
GLU
34
A
GLU
34
A
ASN
83
A
ASN
83
A
ILE
85
A
ILE
85
A
GLN
18
A
GLN
18
A
ASP
25
A
ASP
25
A
PRO
9
A
PRO
9
A
ILE
15
A
ILE
15
A
GLU
65
A
GLU
65
A
ILE
66
A
ILE
66
B
LYS
43
B
LYS
43
B
GLY
49
B
GLY
49
B
GLY
52
B
GLY
52
B
ILE
66
B
ILE
66
B
HIS
69
B
HIS
69
B
GLY
78
B
GLY
78
B
THR
31
B
THR
31
B
GLU
34
B
GLU
34
B
ASN
83
B
ASN
83
B
ILE
85
B
ILE
85
B
GLN
18
B
GLN
18
B
ASP
25
B
ASP
25
B
PRO
9
B
PRO
9
B
ILE
15
B
ILE
15
B
GLU
65
B
GLU
65
B
ILE
66
B
ILE
66
A
PRO
1
A
PRO
1
A
THR
4
A
THR
4
B
THR
96
B
THR
96
B
PHE
99
B
PHE
99
A
THR
96
A
THR
96
A
PHE
99
A
PHE
99
B
PRO
1
B
PRO
1
B
THR
4
B
THR
4
BINDING SITE FOR RESIDUE SO4 A 502
A
SO4
502
Software
2
BINDING SITE FOR RESIDUE SO4 A 503
A
SO4
503
Software
6
BINDING SITE FOR RESIDUE SO4 B 501
B
SO4
501
Software
5
BINDING SITE FOR CHAIN C OF CYCLIC PEPTIDE INHIBITOR
Software
22
A
PRO
1
A
PRO
1
2
1_555
A
HIS
69
A
HIS
69
2
1_555
A
ARG
14
A
ARG
14
6
1_555
B
ARG
14
B
ARG
14
6
1_455
B
ILE
15
B
ILE
15
6
1_455
B
GLY
16
B
GLY
16
6
1_455
B
GLY
17
B
GLY
17
6
1_455
B
HOH
343
H
HOH
6
1_455
A
GLY
68
A
GLY
68
5
3_545
A
HIS
69
A
HIS
69
5
3_545
A
LYS
70
A
LYS
70
5
3_545
B
PRO
1
B
PRO
1
5
2_554
B
LYS
55
B
LYS
55
5
1_555
A
ASP
25
A
ASP
25
22
1_555
A
GLY
27
A
GLY
27
22
1_555
A
ALA
28
A
ALA
28
22
1_555
A
ASP
29
A
ASP
29
22
1_555
A
ASP
30
A
ASP
30
22
1_555
A
GLY
48
A
GLY
48
22
1_555
A
GLY
49
A
GLY
49
22
1_555
A
ILE
50
A
ILE
50
22
1_555
A
PRO
81
A
PRO
81
22
1_555
A
HOH
352
G
HOH
22
1_555
B
ARG
8
B
ARG
8
22
1_555
B
LEU
23
B
LEU
23
22
1_555
B
ASP
25
B
ASP
25
22
1_555
B
GLY
27
B
GLY
27
22
1_555
B
ALA
28
B
ALA
28
22
1_555
B
ASP
29
B
ASP
29
22
1_555
B
ILE
47
B
ILE
47
22
1_555
B
GLY
48
B
GLY
48
22
1_555
B
GLY
49
B
GLY
49
22
1_555
B
VAL
82
B
VAL
82
22
1_555
B
ILE
84
B
ILE
84
22
1_555
C
HOH
301
I
HOH
22
1_555
19
P 21 21 21