0.016787
0.000000
0.000000
0.000000
0.011485
0.000000
0.000000
0.000000
0.021409
0.00000
0.00000
0.00000
Chen, Z.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
59.570
87.070
46.710
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
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
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
N
C
N
387
N
O
N
388
N
O
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
N
N
397
S
C
N
398
N
C
N
399
N
O
N
400
R
C
N
401
N
O
N
402
N
C
N
403
N
O
N
404
N
H
N
405
N
H
N
406
N
H
N
407
N
H
N
408
N
H
N
409
N
H
N
410
N
H
N
411
N
H
N
412
N
H
N
413
N
N
N
414
S
C
N
415
N
C
N
416
N
O
N
417
N
C
Y
418
N
C
Y
419
N
C
Y
420
N
C
Y
421
N
N
Y
422
N
C
Y
423
N
C
Y
424
N
C
Y
425
N
C
Y
426
N
C
N
427
N
O
N
428
N
H
N
429
N
H
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
N
N
441
S
C
N
442
N
C
N
443
N
O
N
444
N
C
Y
445
N
C
Y
446
N
C
Y
447
N
C
Y
448
N
C
Y
449
N
C
Y
450
N
C
N
451
N
O
N
452
N
O
N
453
N
H
N
454
N
H
N
455
N
H
N
456
N
H
N
457
N
H
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
N
N
465
S
C
N
466
N
C
N
467
N
O
N
468
N
C
N
469
N
C
N
470
N
C
N
471
N
O
N
472
N
H
N
473
N
H
N
474
N
H
N
475
N
H
N
476
N
H
N
477
N
H
N
478
N
H
N
479
N
H
N
480
N
H
N
481
N
H
N
482
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
doub
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
sing
N
404
N
sing
N
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
doub
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
Y
413
N
doub
Y
414
N
sing
Y
415
N
sing
N
416
N
sing
Y
417
N
doub
Y
418
N
sing
Y
419
N
sing
N
420
N
sing
Y
421
N
sing
Y
422
N
doub
N
423
N
sing
Y
424
N
doub
N
425
N
sing
Y
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
N
430
N
sing
N
431
N
sing
N
432
N
sing
N
433
N
sing
N
434
N
sing
N
435
N
sing
N
436
N
doub
N
437
N
sing
N
438
N
sing
N
439
N
sing
N
440
N
sing
Y
441
N
doub
Y
442
N
sing
Y
443
N
sing
N
444
N
sing
Y
445
N
doub
N
446
N
sing
Y
447
N
doub
N
448
N
sing
Y
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
N
459
N
sing
N
460
N
doub
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
sing
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
269
26344
26348
7929352
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/pdb1hsg/pdb
pdb_00001hsg
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
x-ray
1
1.0
NY5 ISOLATE
10803.756
HIV-1 PROTEASE
3.4.23.-
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
127
nat
water
no
no
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
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
HIV-1 PROTEASE FROM THE NY5 ISOLATE
11676
Human immunodeficiency virus 1
562
Escherichia coli
2.80
56.10
chem_comp_atom
chem_comp_bond
database_2
pdbx_database_status
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Other
1
0
1996-04-03
1
1
2008-03-24
1
2
2011-07-13
1
3
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Y
BNL
1995-03-31
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 MONOHYDRATE.
MK1
902
2
MK1
MK1
902
B
HOH
305
3
HOH
HOH
305
A
HOH
307
3
HOH
HOH
307
A
HOH
309
3
HOH
HOH
309
A
HOH
314
3
HOH
HOH
314
A
HOH
315
3
HOH
HOH
315
A
HOH
324
3
HOH
HOH
324
A
HOH
325
3
HOH
HOH
325
A
HOH
327
3
HOH
HOH
327
A
HOH
328
3
HOH
HOH
328
A
HOH
329
3
HOH
HOH
329
A
HOH
330
3
HOH
HOH
330
A
HOH
331
3
HOH
HOH
331
A
HOH
332
3
HOH
HOH
332
A
HOH
335
3
HOH
HOH
335
A
HOH
341
3
HOH
HOH
341
A
HOH
342
3
HOH
HOH
342
A
HOH
344
3
HOH
HOH
344
A
HOH
345
3
HOH
HOH
345
A
HOH
357
3
HOH
HOH
357
A
HOH
373
3
HOH
HOH
373
A
HOH
384
3
HOH
HOH
384
A
HOH
386
3
HOH
HOH
386
A
HOH
389
3
HOH
HOH
389
A
HOH
391
3
HOH
HOH
391
A
HOH
394
3
HOH
HOH
394
A
HOH
401
3
HOH
HOH
401
A
HOH
406
3
HOH
HOH
406
A
HOH
408
3
HOH
HOH
408
A
HOH
416
3
HOH
HOH
416
A
HOH
420
3
HOH
HOH
420
A
HOH
422
3
HOH
HOH
422
A
HOH
439
3
HOH
HOH
439
A
HOH
457
3
HOH
HOH
457
A
HOH
468
3
HOH
HOH
468
A
HOH
501
3
HOH
HOH
501
A
HOH
503
3
HOH
HOH
503
A
HOH
510
3
HOH
HOH
510
A
HOH
524
3
HOH
HOH
524
A
HOH
529
3
HOH
HOH
529
A
HOH
553
3
HOH
HOH
553
A
HOH
561
3
HOH
HOH
561
A
HOH
567
3
HOH
HOH
567
A
HOH
572
3
HOH
HOH
572
A
HOH
575
3
HOH
HOH
575
A
HOH
301
3
HOH
HOH
301
B
HOH
303
3
HOH
HOH
303
B
HOH
304
3
HOH
HOH
304
B
HOH
306
3
HOH
HOH
306
B
HOH
308
3
HOH
HOH
308
B
HOH
312
3
HOH
HOH
312
B
HOH
313
3
HOH
HOH
313
B
HOH
316
3
HOH
HOH
316
B
HOH
317
3
HOH
HOH
317
B
HOH
318
3
HOH
HOH
318
B
HOH
319
3
HOH
HOH
319
B
HOH
321
3
HOH
HOH
321
B
HOH
323
3
HOH
HOH
323
B
HOH
326
3
HOH
HOH
326
B
HOH
333
3
HOH
HOH
333
B
HOH
334
3
HOH
HOH
334
B
HOH
338
3
HOH
HOH
338
B
HOH
339
3
HOH
HOH
339
B
HOH
340
3
HOH
HOH
340
B
HOH
346
3
HOH
HOH
346
B
HOH
347
3
HOH
HOH
347
B
HOH
348
3
HOH
HOH
348
B
HOH
349
3
HOH
HOH
349
B
HOH
350
3
HOH
HOH
350
B
HOH
354
3
HOH
HOH
354
B
HOH
355
3
HOH
HOH
355
B
HOH
356
3
HOH
HOH
356
B
HOH
358
3
HOH
HOH
358
B
HOH
359
3
HOH
HOH
359
B
HOH
360
3
HOH
HOH
360
B
HOH
362
3
HOH
HOH
362
B
HOH
364
3
HOH
HOH
364
B
HOH
366
3
HOH
HOH
366
B
HOH
367
3
HOH
HOH
367
B
HOH
369
3
HOH
HOH
369
B
HOH
370
3
HOH
HOH
370
B
HOH
374
3
HOH
HOH
374
B
HOH
375
3
HOH
HOH
375
B
HOH
376
3
HOH
HOH
376
B
HOH
377
3
HOH
HOH
377
B
HOH
379
3
HOH
HOH
379
B
HOH
381
3
HOH
HOH
381
B
HOH
383
3
HOH
HOH
383
B
HOH
387
3
HOH
HOH
387
B
HOH
388
3
HOH
HOH
388
B
HOH
390
3
HOH
HOH
390
B
HOH
392
3
HOH
HOH
392
B
HOH
393
3
HOH
HOH
393
B
HOH
395
3
HOH
HOH
395
B
HOH
400
3
HOH
HOH
400
B
HOH
405
3
HOH
HOH
405
B
HOH
410
3
HOH
HOH
410
B
HOH
414
3
HOH
HOH
414
B
HOH
419
3
HOH
HOH
419
B
HOH
425
3
HOH
HOH
425
B
HOH
430
3
HOH
HOH
430
B
HOH
436
3
HOH
HOH
436
B
HOH
443
3
HOH
HOH
443
B
HOH
444
3
HOH
HOH
444
B
HOH
461
3
HOH
HOH
461
B
HOH
469
3
HOH
HOH
469
B
HOH
471
3
HOH
HOH
471
B
HOH
500
3
HOH
HOH
500
B
HOH
502
3
HOH
HOH
502
B
HOH
505
3
HOH
HOH
505
B
HOH
506
3
HOH
HOH
506
B
HOH
509
3
HOH
HOH
509
B
HOH
514
3
HOH
HOH
514
B
HOH
515
3
HOH
HOH
515
B
HOH
517
3
HOH
HOH
517
B
HOH
525
3
HOH
HOH
525
B
HOH
526
3
HOH
HOH
526
B
HOH
531
3
HOH
HOH
531
B
HOH
532
3
HOH
HOH
532
B
HOH
548
3
HOH
HOH
548
B
HOH
549
3
HOH
HOH
549
B
HOH
556
3
HOH
HOH
556
B
HOH
564
3
HOH
HOH
564
B
HOH
568
3
HOH
HOH
568
B
HOH
591
3
HOH
HOH
591
B
HOH
595
3
HOH
HOH
595
B
HOH
613
3
HOH
HOH
613
B
HOH
617
3
HOH
HOH
617
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
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
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
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
SER
37
n
37
SER
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
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
LEU
63
n
63
LEU
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
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
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
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
LYS
14
n
14
LYS
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
SER
37
n
37
SER
37
B
LEU
38
n
38
LEU
38
B
PRO
39
n
39
PRO
39
B
GLY
40
n
40
GLY
40
B
ARG
41
n
41
ARG
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
LEU
63
n
63
LEU
63
B
ILE
64
n
64
ILE
64
B
GLU
65
n
65
GLU
65
B
ILE
66
n
66
ILE
66
B
CYS
67
n
67
CYS
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
CYS
95
n
95
CYS
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
author_and_software_defined_assembly
PISA
2
dimeric
3560
-24
10770
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
O
VAL
11
A
O
VAL
11
A
N
ALA
22
A
N
ALA
22
A
O
LEU
33
A
O
LEU
33
A
N
LEU
76
A
N
LEU
76
A
O
VAL
75
A
O
VAL
75
A
N
TYR
59
A
N
TYR
59
A
O
GLY
52
A
O
GLY
52
A
N
GLY
49
A
N
GLY
49
A
O
ILE
62
A
O
ILE
62
A
N
GLY
73
A
N
GLY
73
A
O
THR
96
A
O
THR
96
B
N
ASN
98
B
N
ASN
98
B
O
VAL
11
B
O
VAL
11
B
N
ALA
22
B
N
ALA
22
B
O
LYS
43
B
O
LYS
43
B
N
GLN
58
B
N
GLN
58
B
O
ARG
57
B
O
ARG
57
B
N
VAL
77
B
N
VAL
77
B
O
ILE
62
B
O
ILE
62
B
N
GLY
73
B
N
GLY
73
1
-8.43
1.40
111.50
103.07
A
A
A
CA
N
CD
PRO
PRO
PRO
1
1
1
N
1
7.84
1.20
103.80
111.64
A
A
A
N
CD
CG
PRO
PRO
PRO
1
1
1
N
1
A
GLU
35
-28.04
110.40
0.1660000
0.1660000
2.0
1
2.0
127
1686
45
0
1514
0.017
1.9
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
CRYSTAL STRUCTURE AT 1.9 ANGSTROMS RESOLUTION OF HUMAN IMMUNODEFICIENCY VIRUS (HIV) II PROTEASE COMPLEXED WITH L-735,524, AN ORALLY BIOAVAILABLE INHIBITOR OF THE HIV PROTEASES
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
A
ARG
87
A
ARG
87
HELX_P
A
LEU
90
A
LEU
90
1
1
4
B
ARG
87
B
ARG
87
HELX_P
B
LEU
90
B
LEU
90
1
2
4
HYDROLASE (ACID PROTEINASE)
HYDROLASE (ACID PROTEINASE)
POL_HV1BR
UNP
1
1
P03367
FFREDLAFLQGKAREFSSEQTRANSPTISSEQTRANSPTRRELQVWGRDNNSLSEAGADRQGTVSFNFPQITLWQRPLVT
IKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQ
IGCTLNFPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRK
LVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGW
KGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYE
LHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEP
VHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARTRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPI
QKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAASRETKLGKAGYVTNRGRQKVVTLTDTT
NQKTELQAIHLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVS
AGIRKVLFLDGIDKAQDEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVDCSPGIWQLDCTHLEGKVI
LVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTIHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVVES
MNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQTKELQKQITKIQNFRVYYRDSRDP
LWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRDYGKQMAGDDCVASRQDED
69
167
1HSG
1
99
P03367
A
1
1
99
69
167
1HSG
1
99
P03367
B
1
1
99
2
4
2
2
2
3
2
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LEU
10
A
LEU
10
A
ILE
15
A
ILE
15
A
GLN
18
A
GLN
18
A
LEU
23
A
LEU
23
A
VAL
32
A
VAL
32
A
GLU
34
A
GLU
34
A
VAL
75
A
VAL
75
A
GLY
78
A
GLY
78
A
GLY
52
A
GLY
52
A
TYR
59
A
TYR
59
A
LYS
43
A
LYS
43
A
GLY
49
A
GLY
49
A
ILE
62
A
ILE
62
A
ILE
66
A
ILE
66
A
HIS
69
A
HIS
69
A
GLY
73
A
GLY
73
A
THR
96
A
THR
96
A
ASN
98
A
ASN
98
B
THR
96
B
THR
96
B
ASN
98
B
ASN
98
B
LEU
10
B
LEU
10
B
ILE
15
B
ILE
15
B
GLN
18
B
GLN
18
B
LEU
23
B
LEU
23
B
LYS
43
B
LYS
43
B
GLY
48
B
GLY
48
B
PHE
53
B
PHE
53
B
TYR
59
B
TYR
59
B
VAL
75
B
VAL
75
B
VAL
77
B
VAL
77
B
ILE
62
B
ILE
62
B
ILE
66
B
ILE
66
B
HIS
69
B
HIS
69
B
GLY
73
B
GLY
73
BINDING SITE FOR RESIDUE MK1 B 902
B
MK1
902
Software
20
A
ARG
8
A
ARG
8
20
1_555
A
ASP
25
A
ASP
25
20
1_555
A
GLY
27
A
GLY
27
20
1_555
A
GLY
48
A
GLY
48
20
1_555
A
GLY
49
A
GLY
49
20
1_555
A
VAL
82
A
VAL
82
20
1_555
B
ARG
8
B
ARG
8
20
1_555
B
ASP
25
B
ASP
25
20
1_555
B
GLY
27
B
GLY
27
20
1_555
B
ALA
28
B
ALA
28
20
1_555
B
ASP
29
B
ASP
29
20
1_555
B
ASP
30
B
ASP
30
20
1_555
B
VAL
32
B
VAL
32
20
1_555
B
GLY
48
B
GLY
48
20
1_555
B
GLY
49
B
GLY
49
20
1_555
B
ILE
50
B
ILE
50
20
1_555
B
PRO
81
B
PRO
81
20
1_555
B
HOH
308
E
HOH
20
1_555
B
HOH
313
E
HOH
20
1_555
B
HOH
444
E
HOH
20
1_555
18
P 21 21 2