0.014229
0.000000
0.002522
0.000000
0.013899
0.000000
0.000000
0.000000
0.014008
0.000000
0.000000
0.000000
Baum, B.
Heine, A.
Klebe, G.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
100.05
90.00
70.280
71.950
72.500
C23 H32 Cl N3 O3
433.971
N-acetyl-3-cyclohexyl-D-alanyl-N-(3-chlorobenzyl)-L-prolinamide
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
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
Na 1
22.990
SODIUM ION
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
C9 H11 N O6 S
261.252
n
O-SULFO-L-TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
C
N
2
N
O
N
3
N
C
N
4
N
C
N
5
N
C
N
6
N
C
N
7
N
C
N
8
N
C
N
9
N
C
N
10
N
N
N
11
R
C
N
12
N
C
N
13
N
C
N
14
N
O
N
15
N
N
N
16
S
C
N
17
N
C
N
18
N
O
N
19
N
C
N
20
N
C
N
21
N
C
N
22
N
N
N
23
N
C
Y
24
N
C
Y
25
N
C
Y
26
N
C
Y
27
N
C
Y
28
N
C
Y
29
N
C
N
30
N
CL
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
H
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
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
N
N
64
S
C
N
65
N
C
N
66
N
O
N
67
N
C
N
68
N
O
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
N
N
77
S
C
N
78
N
C
N
79
N
O
N
80
N
C
N
81
N
C
N
82
N
C
N
83
N
N
N
84
N
C
N
85
N
N
N
86
N
N
N
87
N
O
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
C
N
109
N
O
N
110
N
N
N
111
N
O
N
112
N
H
N
113
N
H
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
N
N
121
S
C
N
122
N
C
N
123
N
O
N
124
N
C
N
125
N
C
N
126
N
O
N
127
N
O
N
128
N
O
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
N
N
137
R
C
N
138
N
C
N
139
N
O
N
140
N
C
N
141
N
S
N
142
N
O
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
N
N
151
S
C
N
152
N
C
N
153
N
O
N
154
N
C
N
155
N
C
N
156
N
C
N
157
N
O
N
158
N
N
N
159
N
O
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
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
N
N
171
S
C
N
172
N
C
N
173
N
O
N
174
N
C
N
175
N
C
N
176
N
C
N
177
N
O
N
178
N
O
N
179
N
O
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
N
N
190
N
C
N
191
N
C
N
192
N
O
N
193
N
O
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
Y
204
N
C
Y
205
N
N
Y
206
N
C
Y
207
N
C
Y
208
N
N
N
209
N
O
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
O
N
221
N
H
N
222
N
H
N
223
N
N
N
224
S
C
N
225
N
C
N
226
N
O
N
227
S
C
N
228
N
C
N
229
N
C
N
230
N
C
N
231
N
O
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
N
N
246
S
C
N
247
N
C
N
248
N
O
N
249
N
C
N
250
N
C
N
251
N
C
N
252
N
C
N
253
N
O
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
H
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
N
N
268
S
C
N
269
N
C
N
270
N
O
N
271
N
C
N
272
N
C
N
273
N
C
N
274
N
C
N
275
N
N
N
276
N
O
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
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
S
N
299
N
C
N
300
N
O
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
NA
N
313
N
N
N
314
S
C
N
315
N
C
N
316
N
O
N
317
N
C
Y
318
N
C
Y
319
N
C
Y
320
N
C
Y
321
N
C
Y
322
N
C
Y
323
N
C
N
324
N
O
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
N
N
337
S
C
N
338
N
C
N
339
N
O
N
340
N
C
N
341
N
C
N
342
N
C
N
343
N
O
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
H
N
353
N
N
N
354
S
C
N
355
N
C
N
356
N
O
N
357
N
C
N
358
N
O
N
359
N
O
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
N
N
368
S
C
N
369
N
C
N
370
N
O
N
371
R
C
N
372
N
O
N
373
N
C
N
374
N
O
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
H
N
383
N
H
N
384
N
N
N
385
S
C
N
386
N
C
N
387
N
O
N
388
N
C
Y
389
N
C
Y
390
N
C
Y
391
N
C
Y
392
N
N
Y
393
N
C
Y
394
N
C
Y
395
N
C
Y
396
N
C
Y
397
N
C
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
H
N
407
N
H
N
408
N
H
N
409
N
H
N
410
N
H
N
411
N
N
N
412
S
C
N
413
N
C
N
414
N
O
N
415
N
C
Y
416
N
C
Y
417
N
C
Y
418
N
C
Y
419
N
C
Y
420
N
C
Y
421
N
C
N
422
N
O
N
423
N
O
N
424
N
H
N
425
N
H
N
426
N
H
N
427
N
H
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
N
N
436
S
C
N
437
N
C
Y
438
N
C
Y
439
N
C
Y
440
N
C
Y
441
N
C
Y
442
N
C
Y
443
N
C
N
444
N
O
N
445
N
S
N
446
N
O
N
447
N
O
N
448
N
O
N
449
N
C
N
450
N
O
N
451
N
O
N
452
N
H
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
N
N
464
S
C
N
465
N
C
N
466
N
O
N
467
N
C
N
468
N
C
N
469
N
C
N
470
N
O
N
471
N
H
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
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
doub
N
7
N
sing
N
8
N
doub
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
doub
N
18
N
sing
N
19
N
sing
Y
20
N
doub
Y
21
N
sing
Y
22
N
sing
Y
23
N
doub
N
24
N
sing
Y
25
N
sing
Y
26
N
doub
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
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
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
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
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
doub
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
doub
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
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
sing
N
109
N
doub
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
doub
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
doub
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
sing
N
153
N
doub
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
doub
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
doub
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
sing
N
180
N
doub
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
doub
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
doub
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
Y
204
N
sing
Y
205
N
doub
Y
206
N
doub
N
207
N
sing
Y
208
N
sing
N
209
N
sing
Y
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
doub
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
sing
N
243
N
doub
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
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
doub
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
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
doub
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
Y
312
N
doub
Y
313
N
sing
Y
314
N
sing
N
315
N
sing
Y
316
N
doub
N
317
N
sing
Y
318
N
doub
N
319
N
sing
Y
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
doub
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
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
doub
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
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
doub
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
Y
381
N
doub
Y
382
N
sing
Y
383
N
sing
N
384
N
sing
Y
385
N
doub
Y
386
N
sing
Y
387
N
sing
N
388
N
sing
Y
389
N
sing
Y
390
N
doub
N
391
N
sing
Y
392
N
doub
N
393
N
sing
Y
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
doub
N
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
sing
Y
409
N
doub
Y
410
N
sing
Y
411
N
sing
N
412
N
sing
Y
413
N
doub
N
414
N
sing
Y
415
N
doub
N
416
N
sing
Y
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
N
424
N
sing
N
425
N
sing
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
N
430
N
sing
Y
431
N
doub
Y
432
N
sing
Y
433
N
sing
N
434
N
sing
Y
435
N
doub
N
436
N
sing
Y
437
N
doub
N
438
N
sing
Y
439
N
sing
N
440
N
sing
N
441
N
sing
N
442
N
sing
N
443
N
doub
N
444
N
doub
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
doub
N
457
N
sing
N
458
N
sing
N
459
N
sing
N
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
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
391
552
564
10.1016/j.jmb.2009.06.016
19520086
Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin.
2009
10.2210/pdb3f68/pdb
pdb_00003f68
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
110
1
CCD
2008-10-13
ADSC QUANTUM 210
SINGLE WAVELENGTH
M
x-ray
1
0.933
1.0
ID14-1
ESRF
0.933
SYNCHROTRON
ESRF BEAMLINE ID14-1
4096.534
Prothrombin
3.4.21.5
UNP residues 328-363, Thrombin light chain
1
nat
polymer
29780.219
Prothrombin
3.4.21.5
UNP residues 364-622, Thrombin heavy chain
1
nat
polymer
1420.451
Hirudin variant-2
UNP residues 61-71
1
syn
polymer
433.971
N-acetyl-3-cyclohexyl-D-alanyl-N-(3-chlorobenzyl)-L-prolinamide
1
syn
non-polymer
22.990
SODIUM ION
2
syn
non-polymer
18.015
water
104
nat
water
Coagulation factor II, Activation peptide fragment 1, Activation peptide fragment 2, Thrombin light chain, Thrombin heavy chain
Coagulation factor II, Activation peptide fragment 1, Activation peptide fragment 2, Thrombin light chain, Thrombin heavy chain
no
no
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
L
polypeptide(L)
no
no
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISM
LEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL
QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISM
LEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL
QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE
H
polypeptide(L)
no
yes
GDFEEIPEE(TYS)L
GDFEEIPEEYL
I
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
human
sample
9606
Homo sapiens
human
sample
9606
Homo sapiens
1
2.33
51.89
VAPOR DIFFUSION, HANGING DROP
7.5
Phosphate Buffer, Sodium Chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
277
software
software
struct_conn
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_site
chem_comp_atom
chem_comp_bond
repository
Initial release
Atomic model
Database references
Derived calculations
Non-polymer description
Structure summary
Version format compliance
Other
Structure summary
Refinement description
Data collection
Derived calculations
Refinement description
Data collection
Database references
Derived calculations
Refinement description
Data collection
1
0
2009-10-20
1
1
2011-07-13
1
2
2012-12-12
1
3
2016-10-26
1
4
2017-10-25
1
5
2019-07-24
1
6
2023-09-06
1
7
2023-11-15
_software.name
_software.classification
_software.name
_software.version
_struct_conn.pdbx_leaving_atom_flag
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr2_auth_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
_chem_comp_atom.atom_id
_chem_comp_bond.atom_id_2
RCSB
Y
RCSB
2008-11-05
REL
REL
91U
N-acetyl-3-cyclohexyl-D-alanyl-N-(3-chlorobenzyl)-L-prolinamide
NA
SODIUM ION
HOH
water
Synthetic Fragment of Hirudin from Hirudo Medicinalis
6421
Hirudo Medicinalis
sample
1H8D
PDB entry 1H8D
PDB
experimental model
Thrombin inhibitor
N-acetyl-3-cyclohexyl-D-alanyl-N-(3-chlorobenzyl)-L-prolinamide
Peptide-like
91U
901
4
91U
91U
901
H
NA
902
5
NA
NA
902
H
NA
903
5
NA
NA
903
H
HOH
1006
6
HOH
HOH
1006
L
HOH
1012
6
HOH
HOH
1012
L
HOH
1024
6
HOH
HOH
1024
L
HOH
1026
6
HOH
HOH
1026
L
HOH
1056
6
HOH
HOH
1056
L
HOH
1060
6
HOH
HOH
1060
L
HOH
1064
6
HOH
HOH
1064
L
HOH
1073
6
HOH
HOH
1073
L
HOH
1074
6
HOH
HOH
1074
L
HOH
1080
6
HOH
HOH
1080
L
HOH
1085
6
HOH
HOH
1085
L
HOH
1001
6
HOH
HOH
1001
H
HOH
1002
6
HOH
HOH
1002
H
HOH
1003
6
HOH
HOH
1003
H
HOH
1004
6
HOH
HOH
1004
H
HOH
1005
6
HOH
HOH
1005
H
HOH
1007
6
HOH
HOH
1007
H
HOH
1008
6
HOH
HOH
1008
H
HOH
1009
6
HOH
HOH
1009
H
HOH
1010
6
HOH
HOH
1010
H
HOH
1011
6
HOH
HOH
1011
H
HOH
1013
6
HOH
HOH
1013
H
HOH
1014
6
HOH
HOH
1014
H
HOH
1015
6
HOH
HOH
1015
H
HOH
1016
6
HOH
HOH
1016
H
HOH
1017
6
HOH
HOH
1017
H
HOH
1018
6
HOH
HOH
1018
H
HOH
1019
6
HOH
HOH
1019
H
HOH
1020
6
HOH
HOH
1020
H
HOH
1021
6
HOH
HOH
1021
H
HOH
1022
6
HOH
HOH
1022
H
HOH
1023
6
HOH
HOH
1023
H
HOH
1025
6
HOH
HOH
1025
H
HOH
1027
6
HOH
HOH
1027
H
HOH
1028
6
HOH
HOH
1028
H
HOH
1029
6
HOH
HOH
1029
H
HOH
1030
6
HOH
HOH
1030
H
HOH
1031
6
HOH
HOH
1031
H
HOH
1032
6
HOH
HOH
1032
H
HOH
1033
6
HOH
HOH
1033
H
HOH
1034
6
HOH
HOH
1034
H
HOH
1035
6
HOH
HOH
1035
H
HOH
1036
6
HOH
HOH
1036
H
HOH
1037
6
HOH
HOH
1037
H
HOH
1038
6
HOH
HOH
1038
H
HOH
1039
6
HOH
HOH
1039
H
HOH
1040
6
HOH
HOH
1040
H
HOH
1041
6
HOH
HOH
1041
H
HOH
1042
6
HOH
HOH
1042
H
HOH
1043
6
HOH
HOH
1043
H
HOH
1044
6
HOH
HOH
1044
H
HOH
1045
6
HOH
HOH
1045
H
HOH
1046
6
HOH
HOH
1046
H
HOH
1047
6
HOH
HOH
1047
H
HOH
1048
6
HOH
HOH
1048
H
HOH
1049
6
HOH
HOH
1049
H
HOH
1050
6
HOH
HOH
1050
H
HOH
1051
6
HOH
HOH
1051
H
HOH
1052
6
HOH
HOH
1052
H
HOH
1053
6
HOH
HOH
1053
H
HOH
1054
6
HOH
HOH
1054
H
HOH
1055
6
HOH
HOH
1055
H
HOH
1057
6
HOH
HOH
1057
H
HOH
1058
6
HOH
HOH
1058
H
HOH
1059
6
HOH
HOH
1059
H
HOH
1061
6
HOH
HOH
1061
H
HOH
1062
6
HOH
HOH
1062
H
HOH
1063
6
HOH
HOH
1063
H
HOH
1065
6
HOH
HOH
1065
H
HOH
1066
6
HOH
HOH
1066
H
HOH
1067
6
HOH
HOH
1067
H
HOH
1068
6
HOH
HOH
1068
H
HOH
1069
6
HOH
HOH
1069
H
HOH
1070
6
HOH
HOH
1070
H
HOH
1071
6
HOH
HOH
1071
H
HOH
1072
6
HOH
HOH
1072
H
HOH
1075
6
HOH
HOH
1075
H
HOH
1076
6
HOH
HOH
1076
H
HOH
1077
6
HOH
HOH
1077
H
HOH
1078
6
HOH
HOH
1078
H
HOH
1079
6
HOH
HOH
1079
H
HOH
1081
6
HOH
HOH
1081
H
HOH
1082
6
HOH
HOH
1082
H
HOH
1083
6
HOH
HOH
1083
H
HOH
1084
6
HOH
HOH
1084
H
HOH
1086
6
HOH
HOH
1086
H
HOH
1087
6
HOH
HOH
1087
H
HOH
1088
6
HOH
HOH
1088
H
HOH
1089
6
HOH
HOH
1089
H
HOH
1090
6
HOH
HOH
1090
H
HOH
1091
6
HOH
HOH
1091
H
HOH
1092
6
HOH
HOH
1092
H
HOH
1093
6
HOH
HOH
1093
H
HOH
1094
6
HOH
HOH
1094
H
HOH
1096
6
HOH
HOH
1096
H
HOH
1097
6
HOH
HOH
1097
H
HOH
1098
6
HOH
HOH
1098
H
HOH
1099
6
HOH
HOH
1099
H
HOH
1101
6
HOH
HOH
1101
H
HOH
1102
6
HOH
HOH
1102
H
HOH
1103
6
HOH
HOH
1103
H
HOH
1104
6
HOH
HOH
1104
H
HOH
1105
6
HOH
HOH
1105
H
HOH
1106
6
HOH
HOH
1106
H
n
1
-5
L
n
2
-4
L
n
3
-3
L
n
4
-2
L
n
5
-1
L
n
6
0
L
ALA
1
n
7
B
ALA
1
L
ASP
1
n
8
A
ASP
1
L
CYS
1
n
9
CYS
1
L
GLY
2
n
10
GLY
2
L
LEU
3
n
11
LEU
3
L
ARG
4
n
12
ARG
4
L
PRO
5
n
13
PRO
5
L
LEU
6
n
14
LEU
6
L
PHE
7
n
15
PHE
7
L
GLU
8
n
16
GLU
8
L
LYS
9
n
17
LYS
9
L
LYS
10
n
18
LYS
10
L
SER
11
n
19
SER
11
L
LEU
12
n
20
LEU
12
L
GLU
13
n
21
GLU
13
L
ASP
14
n
22
ASP
14
L
LYS
14
n
23
A
LYS
14
L
THR
14
n
24
B
THR
14
L
GLU
14
n
25
C
GLU
14
L
ARG
14
n
26
D
ARG
14
L
GLU
14
n
27
E
GLU
14
L
LEU
14
n
28
F
LEU
14
L
LEU
14
n
29
G
LEU
14
L
GLU
14
n
30
H
GLU
14
L
SER
14
n
31
I
SER
14
L
TYR
14
n
32
J
TYR
14
L
ILE
14
n
33
K
ILE
14
L
n
34
15
L
n
35
16
L
n
36
17
L
ILE
16
n
1
ILE
16
H
VAL
17
n
2
VAL
17
H
GLU
18
n
3
GLU
18
H
GLY
19
n
4
GLY
19
H
SER
20
n
5
SER
20
H
ASP
21
n
6
ASP
21
H
ALA
22
n
7
ALA
22
H
GLU
23
n
8
GLU
23
H
ILE
24
n
9
ILE
24
H
GLY
25
n
10
GLY
25
H
MET
26
n
11
MET
26
H
SER
27
n
12
SER
27
H
PRO
28
n
13
PRO
28
H
TRP
29
n
14
TRP
29
H
GLN
30
n
15
GLN
30
H
VAL
31
n
16
VAL
31
H
MET
32
n
17
MET
32
H
LEU
33
n
18
LEU
33
H
PHE
34
n
19
PHE
34
H
ARG
35
n
20
ARG
35
H
LYS
36
n
21
LYS
36
H
SER
36
n
22
A
SER
36
H
PRO
37
n
23
PRO
37
H
GLN
38
n
24
GLN
38
H
GLU
39
n
25
GLU
39
H
LEU
40
n
26
LEU
40
H
LEU
41
n
27
LEU
41
H
CYS
42
n
28
CYS
42
H
GLY
43
n
29
GLY
43
H
ALA
44
n
30
ALA
44
H
SER
45
n
31
SER
45
H
LEU
46
n
32
LEU
46
H
ILE
47
n
33
ILE
47
H
SER
48
n
34
SER
48
H
ASP
49
n
35
ASP
49
H
ALA
50
n
36
ARG
50
H
TRP
51
n
37
TRP
51
H
VAL
52
n
38
VAL
52
H
LEU
53
n
39
LEU
53
H
THR
54
n
40
THR
54
H
ALA
55
n
41
ALA
55
H
ALA
56
n
42
ALA
56
H
HIS
57
n
43
HIS
57
H
CYS
58
n
44
CYS
58
H
LEU
59
n
45
LEU
59
H
LEU
60
n
46
LEU
60
H
TYR
60
n
47
A
TYR
60
H
PRO
60
n
48
B
PRO
60
H
PRO
60
n
49
C
PRO
60
H
TRP
60
n
50
D
TRP
60
H
ASP
60
n
51
E
ASP
60
H
LYS
60
n
52
F
LYS
60
H
ASN
60
n
53
G
ASN
60
H
PHE
60
n
54
H
PHE
60
H
THR
60
n
55
I
THR
60
H
GLU
61
n
56
GLU
61
H
ALA
62
n
57
ASN
62
H
ASP
63
n
58
ASP
63
H
LEU
64
n
59
LEU
64
H
LEU
65
n
60
LEU
65
H
VAL
66
n
61
VAL
66
H
ARG
67
n
62
ARG
67
H
ILE
68
n
63
ILE
68
H
GLY
69
n
64
GLY
69
H
LYS
70
n
65
LYS
70
H
HIS
71
n
66
HIS
71
H
SER
72
n
67
SER
72
H
ARG
73
n
68
ARG
73
H
THR
74
n
69
THR
74
H
ALA
75
n
70
ARG
75
H
TYR
76
n
71
TYR
76
H
GLU
77
n
72
GLU
77
H
ARG
77
n
73
A
ARG
77
H
ASN
78
n
74
ASN
78
H
ILE
79
n
75
ILE
79
H
GLU
80
n
76
GLU
80
H
LYS
81
n
77
LYS
81
H
ILE
82
n
78
ILE
82
H
SER
83
n
79
SER
83
H
MET
84
n
80
MET
84
H
LEU
85
n
81
LEU
85
H
GLU
86
n
82
GLU
86
H
ALA
87
n
83
LYS
87
H
ILE
88
n
84
ILE
88
H
TYR
89
n
85
TYR
89
H
ILE
90
n
86
ILE
90
H
HIS
91
n
87
HIS
91
H
PRO
92
n
88
PRO
92
H
ARG
93
n
89
ARG
93
H
TYR
94
n
90
TYR
94
H
ASN
95
n
91
ASN
95
H
TRP
96
n
92
TRP
96
H
ARG
97
n
93
ARG
97
H
GLU
97
n
94
A
GLU
97
H
ASN
98
n
95
ASN
98
H
LEU
99
n
96
LEU
99
H
ASP
100
n
97
ASP
100
H
ARG
101
n
98
ARG
101
H
ASP
102
n
99
ASP
102
H
ILE
103
n
100
ILE
103
H
ALA
104
n
101
ALA
104
H
LEU
105
n
102
LEU
105
H
MET
106
n
103
MET
106
H
LYS
107
n
104
LYS
107
H
LEU
108
n
105
LEU
108
H
LYS
109
n
106
LYS
109
H
LYS
110
n
107
LYS
110
H
PRO
111
n
108
PRO
111
H
VAL
112
n
109
VAL
112
H
ALA
113
n
110
ALA
113
H
PHE
114
n
111
PHE
114
H
SER
115
n
112
SER
115
H
ASP
116
n
113
ASP
116
H
TYR
117
n
114
TYR
117
H
ILE
118
n
115
ILE
118
H
HIS
119
n
116
HIS
119
H
PRO
120
n
117
PRO
120
H
VAL
121
n
118
VAL
121
H
CYS
122
n
119
CYS
122
H
LEU
123
n
120
LEU
123
H
PRO
124
n
121
PRO
124
H
ASP
125
n
122
ASP
125
H
ARG
126
n
123
ARG
126
H
GLU
127
n
124
GLU
127
H
THR
128
n
125
THR
128
H
ALA
129
n
126
ALA
129
H
ALA
129
n
127
A
ALA
129
H
SER
129
n
128
B
SER
129
H
LEU
129
n
129
C
LEU
129
H
LEU
130
n
130
LEU
130
H
GLN
131
n
131
GLN
131
H
ALA
132
n
132
ALA
132
H
GLY
133
n
133
GLY
133
H
TYR
134
n
134
TYR
134
H
LYS
135
n
135
LYS
135
H
GLY
136
n
136
GLY
136
H
ARG
137
n
137
ARG
137
H
VAL
138
n
138
VAL
138
H
THR
139
n
139
THR
139
H
GLY
140
n
140
GLY
140
H
TRP
141
n
141
TRP
141
H
GLY
142
n
142
GLY
142
H
ASN
143
n
143
ASN
143
H
LEU
144
n
144
LEU
144
H
LYS
145
n
145
LYS
145
H
GLU
146
n
146
GLU
146
H
n
147
A
146
H
n
148
B
146
H
n
149
C
146
H
n
150
D
146
H
n
151
E
146
H
n
152
F
146
H
n
153
G
146
H
n
154
H
146
H
n
155
I
146
H
GLN
151
n
156
GLN
151
H
PRO
152
n
157
PRO
152
H
SER
153
n
158
SER
153
H
VAL
154
n
159
VAL
154
H
LEU
155
n
160
LEU
155
H
GLN
156
n
161
GLN
156
H
VAL
157
n
162
VAL
157
H
VAL
158
n
163
VAL
158
H
ASN
159
n
164
ASN
159
H
LEU
160
n
165
LEU
160
H
PRO
161
n
166
PRO
161
H
ILE
162
n
167
ILE
162
H
VAL
163
n
168
VAL
163
H
GLU
164
n
169
GLU
164
H
ARG
165
n
170
ARG
165
H
PRO
166
n
171
PRO
166
H
VAL
167
n
172
VAL
167
H
CYS
168
n
173
CYS
168
H
LYS
169
n
174
LYS
169
H
ASP
170
n
175
ASP
170
H
SER
171
n
176
SER
171
H
THR
172
n
177
THR
172
H
ARG
173
n
178
ARG
173
H
ILE
174
n
179
ILE
174
H
ARG
175
n
180
ARG
175
H
ILE
176
n
181
ILE
176
H
THR
177
n
182
THR
177
H
ASP
178
n
183
ASP
178
H
ASN
179
n
184
ASN
179
H
MET
180
n
185
MET
180
H
PHE
181
n
186
PHE
181
H
CYS
182
n
187
CYS
182
H
ALA
183
n
188
ALA
183
H
GLY
184
n
189
GLY
184
H
TYR
184
n
190
A
TYR
184
H
LYS
185
n
191
LYS
185
H
PRO
186
n
192
PRO
186
H
ASP
186
n
193
A
ASP
186
H
GLU
186
n
194
B
GLU
186
H
GLY
186
n
195
C
GLY
186
H
LYS
186
n
196
D
LYS
186
H
ARG
187
n
197
ARG
187
H
GLY
188
n
198
GLY
188
H
ASP
189
n
199
ASP
189
H
ALA
190
n
200
ALA
190
H
CYS
191
n
201
CYS
191
H
GLU
192
n
202
GLU
192
H
GLY
193
n
203
GLY
193
H
ASP
194
n
204
ASP
194
H
SER
195
n
205
SER
195
H
GLY
196
n
206
GLY
196
H
GLY
197
n
207
GLY
197
H
PRO
198
n
208
PRO
198
H
PHE
199
n
209
PHE
199
H
VAL
200
n
210
VAL
200
H
MET
201
n
211
MET
201
H
LYS
202
n
212
LYS
202
H
SER
203
n
213
SER
203
H
PRO
204
n
214
PRO
204
H
PHE
204
n
215
A
PHE
204
H
ASN
204
n
216
B
ASN
204
H
ASN
205
n
217
ASN
205
H
ARG
206
n
218
ARG
206
H
TRP
207
n
219
TRP
207
H
TYR
208
n
220
TYR
208
H
GLN
209
n
221
GLN
209
H
MET
210
n
222
MET
210
H
GLY
211
n
223
GLY
211
H
ILE
212
n
224
ILE
212
H
VAL
213
n
225
VAL
213
H
SER
214
n
226
SER
214
H
TRP
215
n
227
TRP
215
H
GLY
216
n
228
GLY
216
H
GLU
217
n
229
GLU
217
H
GLY
219
n
230
GLY
219
H
CYS
220
n
231
CYS
220
H
ASP
221
n
232
ASP
221
H
ARG
221
n
233
A
ARG
221
H
ASP
222
n
234
ASP
222
H
GLY
223
n
235
GLY
223
H
LYS
224
n
236
LYS
224
H
TYR
225
n
237
TYR
225
H
GLY
226
n
238
GLY
226
H
PHE
227
n
239
PHE
227
H
TYR
228
n
240
TYR
228
H
THR
229
n
241
THR
229
H
HIS
230
n
242
HIS
230
H
VAL
231
n
243
VAL
231
H
PHE
232
n
244
PHE
232
H
ARG
233
n
245
ARG
233
H
LEU
234
n
246
LEU
234
H
LYS
235
n
247
LYS
235
H
LYS
236
n
248
LYS
236
H
TRP
237
n
249
TRP
237
H
ILE
238
n
250
ILE
238
H
GLN
239
n
251
GLN
239
H
LYS
240
n
252
LYS
240
H
VAL
241
n
253
VAL
241
H
ILE
242
n
254
ILE
242
H
ASP
243
n
255
ASP
243
H
GLN
244
n
256
GLN
244
H
PHE
245
n
257
PHE
245
H
GLY
246
n
258
GLY
246
H
n
259
247
H
n
1
54
I
ASP
55
n
2
ASP
55
I
PHE
56
n
3
PHE
56
I
GLU
57
n
4
GLU
57
I
ALA
58
n
5
GLU
58
I
ILE
59
n
6
ILE
59
I
PRO
60
n
7
PRO
60
I
ALA
61
n
8
GLU
61
I
ALA
62
n
9
GLU
62
I
TYS
63
n
10
TYS
63
I
n
11
64
I
0.1935
0.2105
0.1778
0.1960
0.2395
0.2563
1173
1730
4.9
5.0
23952
author_and_software_defined_assembly
PISA
3
trimeric
3450
-31
12410
H
LYS
169
B
O
LYS
174
1_555
H
NA
903
F
NA
NA
1_555
H
THR
172
B
O
THR
177
1_555
80.1
H
LYS
169
B
O
LYS
174
1_555
H
NA
903
F
NA
NA
1_555
H
HOH
1023
H
O
HOH
1_555
72.5
H
THR
172
B
O
THR
177
1_555
H
NA
903
F
NA
NA
1_555
H
HOH
1023
H
O
HOH
1_555
77.4
H
LYS
169
B
O
LYS
174
1_555
H
NA
903
F
NA
NA
1_555
H
HOH
1052
H
O
HOH
1_555
171.3
H
THR
172
B
O
THR
177
1_555
H
NA
903
F
NA
NA
1_555
H
HOH
1052
H
O
HOH
1_555
96.2
H
HOH
1023
H
O
HOH
1_555
H
NA
903
F
NA
NA
1_555
H
HOH
1052
H
O
HOH
1_555
99.0
H
LYS
169
B
O
LYS
174
1_555
H
NA
903
F
NA
NA
1_555
H
HOH
1070
H
O
HOH
1_555
93.1
H
THR
172
B
O
THR
177
1_555
H
NA
903
F
NA
NA
1_555
H
HOH
1070
H
O
HOH
1_555
170.2
H
HOH
1023
H
O
HOH
1_555
H
NA
903
F
NA
NA
1_555
H
HOH
1070
H
O
HOH
1_555
93.8
H
HOH
1052
H
O
HOH
1_555
H
NA
903
F
NA
NA
1_555
H
HOH
1070
H
O
HOH
1_555
89.4
A
H
ARG
221
B
O
ARG
233
1_555
H
NA
902
E
NA
NA
1_555
H
LYS
224
B
O
LYS
236
1_555
98.3
A
H
ARG
221
B
O
ARG
233
1_555
H
NA
902
E
NA
NA
1_555
H
HOH
1041
H
O
HOH
1_555
156.5
H
LYS
224
B
O
LYS
236
1_555
H
NA
902
E
NA
NA
1_555
H
HOH
1041
H
O
HOH
1_555
69.3
A
H
ARG
221
B
O
ARG
233
1_555
H
NA
902
E
NA
NA
1_555
H
HOH
1043
H
O
HOH
1_555
99.2
H
LYS
224
B
O
LYS
236
1_555
H
NA
902
E
NA
NA
1_555
H
HOH
1043
H
O
HOH
1_555
80.1
H
HOH
1041
H
O
HOH
1_555
H
NA
902
E
NA
NA
1_555
H
HOH
1043
H
O
HOH
1_555
98.2
A
H
ARG
221
B
O
ARG
233
1_555
H
NA
902
E
NA
NA
1_555
H
HOH
1050
H
O
HOH
1_555
85.6
H
LYS
224
B
O
LYS
236
1_555
H
NA
902
E
NA
NA
1_555
H
HOH
1050
H
O
HOH
1_555
89.2
H
HOH
1041
H
O
HOH
1_555
H
NA
902
E
NA
NA
1_555
H
HOH
1050
H
O
HOH
1_555
74.6
H
HOH
1043
H
O
HOH
1_555
H
NA
902
E
NA
NA
1_555
H
HOH
1050
H
O
HOH
1_555
168.7
A
H
ARG
221
B
O
ARG
233
1_555
H
NA
902
E
NA
NA
1_555
H
HOH
1081
H
O
HOH
1_555
100.1
H
LYS
224
B
O
LYS
236
1_555
H
NA
902
E
NA
NA
1_555
H
HOH
1081
H
O
HOH
1_555
159.2
H
HOH
1041
H
O
HOH
1_555
H
NA
902
E
NA
NA
1_555
H
HOH
1081
H
O
HOH
1_555
90.0
H
HOH
1043
H
O
HOH
1_555
H
NA
902
E
NA
NA
1_555
H
HOH
1081
H
O
HOH
1_555
106.3
H
HOH
1050
H
O
HOH
1_555
H
NA
902
E
NA
NA
1_555
H
HOH
1081
H
O
HOH
1_555
82.6
I
TYS
63
O-SULFO-L-TYROSINE
C
TYS
10
TYR
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
H
N
SER
20
B
N
SER
5
H
O
VAL
157
B
O
VAL
162
H
O
VAL
158
B
O
VAL
163
H
N
VAL
138
B
N
VAL
138
H
N
ARG
137
B
N
ARG
137
H
O
VAL
200
B
O
VAL
210
H
N
MET
201
B
N
MET
211
H
O
TYR
208
B
O
TYR
220
H
N
TRP
215
B
N
TRP
227
H
O
PHE
227
B
O
PHE
239
H
O
TYR
228
B
O
TYR
240
H
N
PHE
181
B
N
PHE
186
H
N
ARG
35
B
N
ARG
20
H
O
GLU
39
B
O
GLU
25
H
N
SER
45
B
N
SER
31
H
O
LEU
53
B
O
LEU
39
H
N
VAL
52
B
N
VAL
38
H
O
MET
106
B
O
MET
103
H
O
LEU
105
B
O
LEU
102
H
N
TYR
89
B
N
TYR
85
H
O
SER
83
B
O
SER
79
H
N
VAL
66
B
N
VAL
61
H
O
ARG
67
B
O
ARG
62
H
N
MET
32
B
N
MET
17
A
H
N
TYR
60
B
N
TYR
47
F
H
O
LYS
60
B
O
LYS
52
1
H
HOH
1069
H
HOH
1
H
CG
ARG
50
B
CG
ARG
36
1
Y
1
H
CD
ARG
50
B
CD
ARG
36
1
Y
1
H
NE
ARG
50
B
NE
ARG
36
1
Y
1
H
CZ
ARG
50
B
CZ
ARG
36
1
Y
1
H
NH1
ARG
50
B
NH1
ARG
36
1
Y
1
H
NH2
ARG
50
B
NH2
ARG
36
1
Y
1
H
CG
ASN
62
B
CG
ASN
57
1
Y
1
H
OD1
ASN
62
B
OD1
ASN
57
1
Y
1
H
ND2
ASN
62
B
ND2
ASN
57
1
Y
1
H
CG
ARG
75
B
CG
ARG
70
1
Y
1
H
CD
ARG
75
B
CD
ARG
70
1
Y
1
H
NE
ARG
75
B
NE
ARG
70
1
Y
1
H
CZ
ARG
75
B
CZ
ARG
70
1
Y
1
H
NH1
ARG
75
B
NH1
ARG
70
1
Y
1
H
NH2
ARG
75
B
NH2
ARG
70
1
Y
1
H
CG
LYS
87
B
CG
LYS
83
1
Y
1
H
CD
LYS
87
B
CD
LYS
83
1
Y
1
H
CE
LYS
87
B
CE
LYS
83
1
Y
1
H
NZ
LYS
87
B
NZ
LYS
83
1
Y
1
H
CG
GLN
151
B
CG
GLN
156
1
Y
1
H
CD
GLN
151
B
CD
GLN
156
1
Y
1
H
OE1
GLN
151
B
OE1
GLN
156
1
Y
1
H
NE2
GLN
151
B
NE2
GLN
156
1
Y
A
1
H
CG
ASP
186
B
CG
ASP
193
1
Y
A
1
H
OD1
ASP
186
B
OD1
ASP
193
1
Y
A
1
H
OD2
ASP
186
B
OD2
ASP
193
1
Y
1
H
CG
LYS
236
B
CG
LYS
248
1
Y
1
H
CD
LYS
236
B
CD
LYS
248
1
Y
1
H
CE
LYS
236
B
CE
LYS
248
1
Y
1
H
NZ
LYS
236
B
NZ
LYS
248
1
Y
1
I
CG
GLU
58
C
CG
GLU
5
1
Y
1
I
CD
GLU
58
C
CD
GLU
5
1
Y
1
I
OE1
GLU
58
C
OE1
GLU
5
1
Y
1
I
OE2
GLU
58
C
OE2
GLU
5
1
Y
1
I
CG
GLU
61
C
CG
GLU
8
1
Y
1
I
CD
GLU
61
C
CD
GLU
8
1
Y
1
I
OE1
GLU
61
C
OE1
GLU
8
1
Y
1
I
OE2
GLU
61
C
OE2
GLU
8
1
Y
1
I
CG
GLU
62
C
CG
GLU
9
1
Y
1
I
CD
GLU
62
C
CD
GLU
9
1
Y
1
I
OE1
GLU
62
C
OE1
GLU
9
1
Y
1
I
OE2
GLU
62
C
OE2
GLU
9
1
Y
1
L
THR
-5
A
THR
1
1
Y
1
L
PHE
-4
A
PHE
2
1
Y
1
L
GLY
-3
A
GLY
3
1
Y
1
L
SER
-2
A
SER
4
1
Y
1
L
GLY
-1
A
GLY
5
1
Y
1
L
GLU
0
A
GLU
6
1
Y
1
L
ASP
15
A
ASP
34
1
Y
1
L
GLY
16
A
GLY
35
1
Y
1
L
ARG
17
A
ARG
36
1
Y
A
1
H
THR
146
B
THR
147
1
Y
B
1
H
TRP
146
B
TRP
148
1
Y
C
1
H
THR
146
B
THR
149
1
Y
D
1
H
ALA
146
B
ALA
150
1
Y
E
1
H
ASN
146
B
ASN
151
1
Y
F
1
H
VAL
146
B
VAL
152
1
Y
G
1
H
GLY
146
B
GLY
153
1
Y
H
1
H
LYS
146
B
LYS
154
1
Y
I
1
H
GLY
146
B
GLY
155
1
Y
1
H
GLU
247
B
GLU
259
1
Y
1
I
GLY
54
C
GLY
1
1
Y
1
I
LEU
64
C
LEU
11
1
Y
1
4.32
0.50
120.30
124.62
L
L
L
NE
CZ
NH1
ARG
ARG
ARG
4
4
4
N
A
A
A
1
5.08
0.50
120.30
125.38
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
77
77
77
N
A
A
A
1
-4.60
0.50
120.30
115.70
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
77
77
77
N
1
L
PHE
7
-131.64
-90.52
1
H
ALA
44
-176.10
-178.31
1
H
SER
48
-163.69
-166.71
A
1
H
TYR
60
-151.09
79.28
1
H
HIS
71
-135.75
-48.70
1
H
ASN
78
71.94
-2.81
1
H
ILE
79
-120.59
-64.56
1
H
LYS
87
-179.45
126.86
1
H
ASN
98
-141.95
10.91
1
H
SER
214
-123.35
-55.67
1
H
ASP
243
-46.92
-70.53
ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
0.2563
0.1960
0.2105
0.2105
1.75
10.00
9701
1730
34856
34856
9498
5.0
97.9
RANDOM
1
FREE R
0.0
MOLECULAR REPLACEMENT
PDB entry 1H8D
ENGH AND HUBER
0
0.00
2421.50
1.75
10.00
104
2420
32
0
2284
0.007
0.025
0.000
0.0282
0.038
0.048
0.009
0.000
0.090
0.000
1.75
29.20
3F68
35166
0.064
0.064
1
11.7
2.4
98.5
0.707
1.75
1.85
1.2
11620
0.707
1
2.3
98.1
refinement
SHELXL-97
refinement
CNS
data collection
MAR345
CCD
data reduction
MOSFLM
data scaling
SCALEPACK
phasing
CNS
Thrombin Inhibition
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
5
N
N
6
N
N
6
N
N
L
PHE
7
A
PHE
15
HELX_P
L
SER
11
A
SER
19
5
1
5
L
THR
14
A
THR
24
HELX_P
L
TYR
14
A
TYR
32
1
2
9
B
J
H
ALA
55
B
ALA
41
HELX_P
H
LEU
59
B
LEU
45
1
3
5
H
PRO
60
B
PRO
48
HELX_P
H
ASP
60
B
ASP
51
5
4
4
B
E
H
THR
60
B
THR
55
HELX_P
H
ASN
62
B
ASN
57
5
5
3
I
H
ASP
125
B
ASP
122
HELX_P
H
LEU
130
B
LEU
130
1
6
9
H
GLU
164
B
GLU
169
HELX_P
H
SER
171
B
SER
176
1
7
8
H
LYS
185
B
LYS
191
HELX_P
H
GLY
186
B
GLY
195
5
8
5
C
H
LEU
234
B
LEU
246
HELX_P
H
GLY
246
B
GLY
258
1
9
13
disulf
2.071
L
CYS
1
A
SG
CYS
9
1_555
H
CYS
122
B
SG
CYS
119
1_555
disulf
2.040
H
CYS
42
B
SG
CYS
28
1_555
H
CYS
58
B
SG
CYS
44
1_555
disulf
2.021
H
CYS
168
B
SG
CYS
173
1_555
H
CYS
182
B
SG
CYS
187
1_555
disulf
2.038
H
CYS
191
B
SG
CYS
201
1_555
H
CYS
220
B
SG
CYS
231
1_555
covale
1.332
both
I
GLU
62
C
C
GLU
9
1_555
I
TYS
63
C
N
TYS
10
1_555
metalc
2.379
H
LYS
169
B
O
LYS
174
1_555
H
NA
903
F
NA
NA
1_555
metalc
2.306
H
THR
172
B
O
THR
177
1_555
H
NA
903
F
NA
NA
1_555
metalc
2.341
A
H
ARG
221
B
O
ARG
233
1_555
H
NA
902
E
NA
NA
1_555
metalc
2.313
H
LYS
224
B
O
LYS
236
1_555
H
NA
902
E
NA
NA
1_555
metalc
2.698
H
NA
902
E
NA
NA
1_555
H
HOH
1041
H
O
HOH
1_555
metalc
2.063
H
NA
902
E
NA
NA
1_555
H
HOH
1043
H
O
HOH
1_555
metalc
2.945
H
NA
902
E
NA
NA
1_555
H
HOH
1050
H
O
HOH
1_555
metalc
2.590
H
NA
902
E
NA
NA
1_555
H
HOH
1081
H
O
HOH
1_555
metalc
2.616
H
NA
903
F
NA
NA
1_555
H
HOH
1023
H
O
HOH
1_555
metalc
2.471
H
NA
903
F
NA
NA
1_555
H
HOH
1052
H
O
HOH
1_555
metalc
2.327
H
NA
903
F
NA
NA
1_555
H
HOH
1070
H
O
HOH
1_555
HYDROLASE/HYDROLASE INHIBITOR
Blood Clotting, Hydrolase Inhibitor, Acute phase, Blood coagulation, Gamma-carboxyglutamic acid, Glycoprotein, Hydrolase, Kringle, Protease, Secreted, Serine protease, Protease inhibitor, Serine protease inhibitor, Sulfation, HYDROLASE-HYDROLASE INHIBITOR COMPLEX
H
SER
36
B
SER
22
A
1
H
PRO
37
B
PRO
23
-3.13
THRB_HUMAN
UNP
1
328
P00734
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
THRB_HUMAN
UNP
2
364
P00734
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISM
LEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL
QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE
HIRV2_HIRME
UNP
3
61
P09945
GDFEEIPEEYL
328
363
3F68
-5
17
P00734
L
1
1
36
364
622
3F68
16
247
P00734
H
2
1
259
61
71
3F68
54
64
P09945
I
3
1
11
7
7
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
H
SER
20
B
SER
5
H
ASP
21
B
ASP
6
H
GLN
156
B
GLN
161
H
PRO
161
B
PRO
166
H
LYS
135
B
LYS
135
H
GLY
140
B
GLY
140
H
PRO
198
B
PRO
208
H
LYS
202
B
LYS
212
H
TRP
207
B
TRP
219
H
TRP
215
B
TRP
227
H
GLY
226
B
GLY
238
H
HIS
230
B
HIS
242
H
MET
180
B
MET
185
H
ALA
183
B
ALA
188
H
GLN
30
B
GLN
15
H
ARG
35
B
ARG
20
H
GLU
39
B
GLU
25
H
LEU
46
B
LEU
32
H
TRP
51
B
TRP
37
H
THR
54
B
THR
40
H
ALA
104
B
ALA
101
H
LEU
108
B
LEU
105
H
LYS
81
B
LYS
77
H
ILE
90
B
ILE
86
H
LEU
64
B
LEU
59
H
ILE
68
B
ILE
63
H
GLN
30
B
GLN
15
H
ARG
35
B
ARG
20
H
LEU
60
B
LEU
46
H
TYR
60
B
TYR
47
A
H
LYS
60
B
LYS
52
H
ASN
60
B
ASN
53
F
G
BINDING SITE FOR RESIDUE 91U H 901
H
91U
901
Software
10
BINDING SITE FOR RESIDUE NA H 902
H
NA
902
Software
6
BINDING SITE FOR RESIDUE NA H 903
H
NA
903
Software
6
BINDING SITE FOR CHAIN I OF HIRUDIN VARIANT-2
Software
12
H
HIS
57
B
HIS
43
10
1_555
H
TYR
60
B
TYR
47
A
10
1_555
H
ALA
190
B
ALA
200
10
1_555
H
SER
195
B
SER
205
10
1_555
H
VAL
213
B
VAL
225
10
1_555
H
SER
214
B
SER
226
10
1_555
H
TRP
215
B
TRP
227
10
1_555
H
GLY
216
B
GLY
228
10
1_555
H
GLU
217
B
GLU
229
10
1_555
H
PHE
227
B
PHE
239
10
1_555
H
ARG
221
B
ARG
233
A
6
1_555
H
LYS
224
B
LYS
236
6
1_555
H
HOH
1041
H
HOH
6
1_555
H
HOH
1043
H
HOH
6
1_555
H
HOH
1050
H
HOH
6
1_555
H
HOH
1081
H
HOH
6
1_555
H
LYS
169
B
LYS
174
6
1_555
H
THR
172
B
THR
177
6
1_555
H
PHE
204
B
PHE
215
A
6
4_546
H
HOH
1023
H
HOH
6
1_555
H
HOH
1052
H
HOH
6
1_555
H
HOH
1070
H
HOH
6
1_555
H
PHE
34
B
PHE
19
12
1_555
H
GLN
38
B
GLN
24
12
1_555
H
GLU
39
B
GLU
25
12
1_555
H
LEU
40
B
LEU
26
12
1_555
H
LEU
65
B
LEU
60
12
1_555
H
ARG
73
B
ARG
68
12
1_555
H
THR
74
B
THR
69
12
1_555
H
ARG
75
B
ARG
70
12
1_555
H
TYR
76
B
TYR
71
12
1_555
H
LYS
81
B
LYS
77
12
1_555
H
ILE
82
B
ILE
78
12
1_555
H
HOH
1044
H
HOH
12
1_555
5
C 1 2 1