0.014297
0.000000
0.002542
0.000000
0.013959
0.000000
0.000000
0.000000
0.014125
0.000000
0.000000
0.000000
Baum, B.
Heine, A.
Klebe, G.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
100.1
90.00
69.95
71.64
71.91
C28 H31 N5 O2
469.578
beta-phenyl-D-phenylalanyl-N-(4-carbamimidoylbenzyl)-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
Y
1
N
C
Y
2
N
C
Y
3
N
C
Y
4
N
C
Y
5
N
C
Y
6
N
C
N
7
N
C
N
8
R
C
N
9
N
C
N
10
N
O
N
11
N
N
Y
12
N
C
Y
13
N
C
Y
14
N
C
Y
15
N
C
Y
16
N
C
Y
17
N
C
N
18
N
N
N
19
S
C
N
20
N
C
N
21
N
O
N
22
N
C
N
23
N
C
N
24
N
C
N
25
N
N
N
26
N
C
Y
27
N
C
Y
28
N
C
Y
29
N
C
Y
30
N
C
N
31
N
C
N
32
N
N
N
33
N
N
Y
34
N
C
Y
35
N
C
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
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
N
N
68
S
C
N
69
N
C
N
70
N
O
N
71
N
C
N
72
N
O
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
N
N
81
S
C
N
82
N
C
N
83
N
O
N
84
N
C
N
85
N
C
N
86
N
C
N
87
N
N
N
88
N
C
N
89
N
N
N
90
N
N
N
91
N
O
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
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
N
N
108
S
C
N
109
N
C
N
110
N
O
N
111
N
C
N
112
N
C
N
113
N
O
N
114
N
N
N
115
N
O
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
O
N
131
N
O
N
132
N
O
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
N
N
141
R
C
N
142
N
C
N
143
N
O
N
144
N
C
N
145
N
S
N
146
N
O
N
147
N
H
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
N
N
155
S
C
N
156
N
C
N
157
N
O
N
158
N
C
N
159
N
C
N
160
N
C
N
161
N
O
N
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
N
N
175
S
C
N
176
N
C
N
177
N
O
N
178
N
C
N
179
N
C
N
180
N
C
N
181
N
O
N
182
N
O
N
183
N
O
N
184
N
H
N
185
N
H
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
N
N
194
N
C
N
195
N
C
N
196
N
O
N
197
N
O
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
N
N
204
S
C
N
205
N
C
N
206
N
O
N
207
N
C
Y
208
N
C
Y
209
N
N
Y
210
N
C
Y
211
N
C
Y
212
N
N
N
213
N
O
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
H
N
222
N
H
N
223
N
H
N
224
N
O
N
225
N
H
N
226
N
H
N
227
N
N
N
228
S
C
N
229
N
C
N
230
N
O
N
231
S
C
N
232
N
C
N
233
N
C
N
234
N
C
N
235
N
O
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
H
N
247
N
H
N
248
N
H
N
249
N
N
N
250
S
C
N
251
N
C
N
252
N
O
N
253
N
C
N
254
N
C
N
255
N
C
N
256
N
C
N
257
N
O
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
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
N
N
272
S
C
N
273
N
C
N
274
N
O
N
275
N
C
N
276
N
C
N
277
N
C
N
278
N
C
N
279
N
N
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
H
N
293
N
H
N
294
N
H
N
295
N
H
N
296
N
N
N
297
S
C
N
298
N
C
N
299
N
O
N
300
N
C
N
301
N
C
N
302
N
S
N
303
N
C
N
304
N
O
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
NA
N
317
N
N
N
318
S
C
N
319
N
C
N
320
N
O
N
321
N
C
Y
322
N
C
Y
323
N
C
Y
324
N
C
Y
325
N
C
Y
326
N
C
Y
327
N
C
N
328
N
O
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
N
N
341
S
C
N
342
N
C
N
343
N
O
N
344
N
C
N
345
N
C
N
346
N
C
N
347
N
O
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
N
N
358
S
C
N
359
N
C
N
360
N
O
N
361
N
C
N
362
N
O
N
363
N
O
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
N
N
372
S
C
N
373
N
C
N
374
N
O
N
375
R
C
N
376
N
O
N
377
N
C
N
378
N
O
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
N
N
389
S
C
N
390
N
C
N
391
N
O
N
392
N
C
Y
393
N
C
Y
394
N
C
Y
395
N
C
Y
396
N
N
Y
397
N
C
Y
398
N
C
Y
399
N
C
Y
400
N
C
Y
401
N
C
N
402
N
O
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
H
N
412
N
H
N
413
N
H
N
414
N
H
N
415
N
N
N
416
S
C
N
417
N
C
N
418
N
O
N
419
N
C
Y
420
N
C
Y
421
N
C
Y
422
N
C
Y
423
N
C
Y
424
N
C
Y
425
N
C
N
426
N
O
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
N
N
440
S
C
N
441
N
C
Y
442
N
C
Y
443
N
C
Y
444
N
C
Y
445
N
C
Y
446
N
C
Y
447
N
C
N
448
N
O
N
449
N
S
N
450
N
O
N
451
N
O
N
452
N
O
N
453
N
C
N
454
N
O
N
455
N
O
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
H
N
465
N
H
N
466
N
H
N
467
N
N
N
468
S
C
N
469
N
C
N
470
N
O
N
471
N
C
N
472
N
C
N
473
N
C
N
474
N
O
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
483
N
H
N
484
N
H
N
485
N
H
Y
1
N
doub
Y
2
N
sing
N
3
N
sing
Y
4
N
doub
N
5
N
sing
Y
6
N
sing
N
7
N
sing
Y
8
N
doub
N
9
N
sing
Y
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
doub
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
doub
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
Y
33
N
doub
Y
34
N
sing
Y
35
N
doub
N
36
N
sing
Y
37
N
sing
N
38
N
sing
Y
39
N
doub
N
40
N
sing
N
41
N
doub
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
Y
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
Y
59
N
doub
Y
60
N
sing
Y
61
N
sing
N
62
N
sing
Y
63
N
doub
N
64
N
sing
Y
65
N
sing
N
66
N
sing
Y
67
N
doub
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
doub
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
doub
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
doub
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
doub
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
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
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
doub
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
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
doub
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
doub
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
doub
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
doub
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
doub
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
Y
209
N
sing
Y
210
N
doub
Y
211
N
doub
N
212
N
sing
Y
213
N
sing
N
214
N
sing
Y
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
sing
N
225
N
sing
N
226
N
sing
N
227
N
doub
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
sing
N
247
N
sing
N
248
N
doub
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
doub
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
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
doub
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
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
doub
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
Y
317
N
doub
Y
318
N
sing
Y
319
N
sing
N
320
N
sing
Y
321
N
doub
N
322
N
sing
Y
323
N
doub
N
324
N
sing
Y
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
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
sing
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
doub
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
sing
N
363
N
sing
N
364
N
sing
N
365
N
doub
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
sing
N
380
N
sing
N
381
N
doub
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
Y
386
N
doub
Y
387
N
sing
Y
388
N
sing
N
389
N
sing
Y
390
N
doub
Y
391
N
sing
Y
392
N
sing
N
393
N
sing
Y
394
N
sing
Y
395
N
doub
N
396
N
sing
Y
397
N
doub
N
398
N
sing
Y
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
sing
N
409
N
doub
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
Y
414
N
doub
Y
415
N
sing
Y
416
N
sing
N
417
N
sing
Y
418
N
doub
N
419
N
sing
Y
420
N
doub
N
421
N
sing
Y
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
N
431
N
sing
N
432
N
sing
N
433
N
sing
N
434
N
sing
N
435
N
sing
Y
436
N
doub
Y
437
N
sing
Y
438
N
sing
N
439
N
sing
Y
440
N
doub
N
441
N
sing
Y
442
N
doub
N
443
N
sing
Y
444
N
sing
N
445
N
sing
N
446
N
sing
N
447
N
sing
N
448
N
doub
N
449
N
doub
N
450
N
sing
N
451
N
sing
N
452
N
doub
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
sing
N
461
N
doub
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
N
472
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/pdb2zo3/pdb
pdb_00002zo3
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
2008-02-16
MAR CCD 165 mm
double crystal
SINGLE WAVELENGTH
M
x-ray
1
0.91841
1.0
14.2
BESSY
0.91841
SYNCHROTRON
BESSY BEAMLINE 14.2
4096.534
Thrombin light chain
3.4.21.5
1
nat
polymer
29780.219
Thrombin heavy chain
3.4.21.5
1
nat
polymer
1420.451
Hirudin variant-1
Residues 54-64
1
syn
polymer
469.578
beta-phenyl-D-phenylalanyl-N-(4-carbamimidoylbenzyl)-L-prolinamide
1
syn
non-polymer
22.990
SODIUM ION
2
syn
non-polymer
18.015
water
195
nat
water
Coagulation factor II
Coagulation factor II
Lepirudin
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
blood plasma
human
sample
9606
Homo sapiens
blood plasma
1
2.51
51.05
VAPOR DIFFUSION, HANGING DROP
7.5
Phosphate Buffer, Sodium Chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
277
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
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
Source and taxonomy
Refinement description
Data collection
Database references
Derived calculations
Refinement description
Data collection
1
0
2009-04-14
1
1
2011-07-13
1
2
2012-12-12
1
3
2016-05-25
1
4
2017-10-11
1
5
2023-11-01
1
6
2023-11-15
_software.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_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
PDBJ
Y
PDBJ
2008-05-05
REL
REL
33U
beta-phenyl-D-phenylalanyl-N-(4-carbamimidoylbenzyl)-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
beta-phenyl-D-phenylalanyl-N-(4-carbamimidoylbenzyl)-L-prolinamide
Peptide-like
33U
2501
4
33U
33U
2501
H
NA
2502
5
NA
NA
2502
H
NA
2503
5
NA
NA
2503
H
HOH
3014
6
HOH
HOH
3014
L
HOH
3019
6
HOH
HOH
3019
L
HOH
3022
6
HOH
HOH
3022
L
HOH
3024
6
HOH
HOH
3024
L
HOH
3033
6
HOH
HOH
3033
L
HOH
3037
6
HOH
HOH
3037
L
HOH
3041
6
HOH
HOH
3041
L
HOH
3046
6
HOH
HOH
3046
L
HOH
3052
6
HOH
HOH
3052
L
HOH
3055
6
HOH
HOH
3055
L
HOH
3064
6
HOH
HOH
3064
L
HOH
3082
6
HOH
HOH
3082
L
HOH
3089
6
HOH
HOH
3089
L
HOH
3111
6
HOH
HOH
3111
L
HOH
3127
6
HOH
HOH
3127
L
HOH
3129
6
HOH
HOH
3129
L
HOH
3144
6
HOH
HOH
3144
L
HOH
3148
6
HOH
HOH
3148
L
HOH
3150
6
HOH
HOH
3150
L
HOH
3153
6
HOH
HOH
3153
L
HOH
3155
6
HOH
HOH
3155
L
HOH
3168
6
HOH
HOH
3168
L
HOH
3173
6
HOH
HOH
3173
L
HOH
3175
6
HOH
HOH
3175
L
HOH
3188
6
HOH
HOH
3188
L
HOH
3192
6
HOH
HOH
3192
L
HOH
3001
6
HOH
HOH
3001
H
HOH
3002
6
HOH
HOH
3002
H
HOH
3003
6
HOH
HOH
3003
H
HOH
3004
6
HOH
HOH
3004
H
HOH
3005
6
HOH
HOH
3005
H
HOH
3006
6
HOH
HOH
3006
H
HOH
3007
6
HOH
HOH
3007
H
HOH
3008
6
HOH
HOH
3008
H
HOH
3009
6
HOH
HOH
3009
H
HOH
3010
6
HOH
HOH
3010
H
HOH
3011
6
HOH
HOH
3011
H
HOH
3012
6
HOH
HOH
3012
H
HOH
3013
6
HOH
HOH
3013
H
HOH
3015
6
HOH
HOH
3015
H
HOH
3016
6
HOH
HOH
3016
H
HOH
3017
6
HOH
HOH
3017
H
HOH
3018
6
HOH
HOH
3018
H
HOH
3020
6
HOH
HOH
3020
H
HOH
3021
6
HOH
HOH
3021
H
HOH
3023
6
HOH
HOH
3023
H
HOH
3025
6
HOH
HOH
3025
H
HOH
3026
6
HOH
HOH
3026
H
HOH
3027
6
HOH
HOH
3027
H
HOH
3028
6
HOH
HOH
3028
H
HOH
3029
6
HOH
HOH
3029
H
HOH
3030
6
HOH
HOH
3030
H
HOH
3031
6
HOH
HOH
3031
H
HOH
3032
6
HOH
HOH
3032
H
HOH
3034
6
HOH
HOH
3034
H
HOH
3035
6
HOH
HOH
3035
H
HOH
3036
6
HOH
HOH
3036
H
HOH
3038
6
HOH
HOH
3038
H
HOH
3039
6
HOH
HOH
3039
H
HOH
3040
6
HOH
HOH
3040
H
HOH
3042
6
HOH
HOH
3042
H
HOH
3043
6
HOH
HOH
3043
H
HOH
3044
6
HOH
HOH
3044
H
HOH
3045
6
HOH
HOH
3045
H
HOH
3047
6
HOH
HOH
3047
H
HOH
3048
6
HOH
HOH
3048
H
HOH
3049
6
HOH
HOH
3049
H
HOH
3050
6
HOH
HOH
3050
H
HOH
3051
6
HOH
HOH
3051
H
HOH
3053
6
HOH
HOH
3053
H
HOH
3054
6
HOH
HOH
3054
H
HOH
3056
6
HOH
HOH
3056
H
HOH
3057
6
HOH
HOH
3057
H
HOH
3058
6
HOH
HOH
3058
H
HOH
3059
6
HOH
HOH
3059
H
HOH
3060
6
HOH
HOH
3060
H
HOH
3061
6
HOH
HOH
3061
H
HOH
3062
6
HOH
HOH
3062
H
HOH
3063
6
HOH
HOH
3063
H
HOH
3065
6
HOH
HOH
3065
H
HOH
3066
6
HOH
HOH
3066
H
HOH
3067
6
HOH
HOH
3067
H
HOH
3068
6
HOH
HOH
3068
H
HOH
3069
6
HOH
HOH
3069
H
HOH
3070
6
HOH
HOH
3070
H
HOH
3071
6
HOH
HOH
3071
H
HOH
3072
6
HOH
HOH
3072
H
HOH
3073
6
HOH
HOH
3073
H
HOH
3074
6
HOH
HOH
3074
H
HOH
3075
6
HOH
HOH
3075
H
HOH
3076
6
HOH
HOH
3076
H
HOH
3077
6
HOH
HOH
3077
H
HOH
3078
6
HOH
HOH
3078
H
HOH
3079
6
HOH
HOH
3079
H
HOH
3080
6
HOH
HOH
3080
H
HOH
3081
6
HOH
HOH
3081
H
HOH
3083
6
HOH
HOH
3083
H
HOH
3084
6
HOH
HOH
3084
H
HOH
3085
6
HOH
HOH
3085
H
HOH
3086
6
HOH
HOH
3086
H
HOH
3087
6
HOH
HOH
3087
H
HOH
3088
6
HOH
HOH
3088
H
HOH
3090
6
HOH
HOH
3090
H
HOH
3091
6
HOH
HOH
3091
H
HOH
3092
6
HOH
HOH
3092
H
HOH
3093
6
HOH
HOH
3093
H
HOH
3094
6
HOH
HOH
3094
H
HOH
3095
6
HOH
HOH
3095
H
HOH
3096
6
HOH
HOH
3096
H
HOH
3097
6
HOH
HOH
3097
H
HOH
3098
6
HOH
HOH
3098
H
HOH
3099
6
HOH
HOH
3099
H
HOH
3100
6
HOH
HOH
3100
H
HOH
3101
6
HOH
HOH
3101
H
HOH
3102
6
HOH
HOH
3102
H
HOH
3103
6
HOH
HOH
3103
H
HOH
3104
6
HOH
HOH
3104
H
HOH
3105
6
HOH
HOH
3105
H
HOH
3106
6
HOH
HOH
3106
H
HOH
3107
6
HOH
HOH
3107
H
HOH
3108
6
HOH
HOH
3108
H
HOH
3109
6
HOH
HOH
3109
H
HOH
3110
6
HOH
HOH
3110
H
HOH
3113
6
HOH
HOH
3113
H
HOH
3114
6
HOH
HOH
3114
H
HOH
3115
6
HOH
HOH
3115
H
HOH
3116
6
HOH
HOH
3116
H
HOH
3117
6
HOH
HOH
3117
H
HOH
3118
6
HOH
HOH
3118
H
HOH
3119
6
HOH
HOH
3119
H
HOH
3120
6
HOH
HOH
3120
H
HOH
3121
6
HOH
HOH
3121
H
HOH
3122
6
HOH
HOH
3122
H
HOH
3123
6
HOH
HOH
3123
H
HOH
3124
6
HOH
HOH
3124
H
HOH
3125
6
HOH
HOH
3125
H
HOH
3126
6
HOH
HOH
3126
H
HOH
3128
6
HOH
HOH
3128
H
HOH
3130
6
HOH
HOH
3130
H
HOH
3131
6
HOH
HOH
3131
H
HOH
3132
6
HOH
HOH
3132
H
HOH
3133
6
HOH
HOH
3133
H
HOH
3134
6
HOH
HOH
3134
H
HOH
3135
6
HOH
HOH
3135
H
HOH
3136
6
HOH
HOH
3136
H
HOH
3137
6
HOH
HOH
3137
H
HOH
3138
6
HOH
HOH
3138
H
HOH
3139
6
HOH
HOH
3139
H
HOH
3140
6
HOH
HOH
3140
H
HOH
3141
6
HOH
HOH
3141
H
HOH
3142
6
HOH
HOH
3142
H
HOH
3143
6
HOH
HOH
3143
H
HOH
3145
6
HOH
HOH
3145
H
HOH
3146
6
HOH
HOH
3146
H
HOH
3147
6
HOH
HOH
3147
H
HOH
3149
6
HOH
HOH
3149
H
HOH
3151
6
HOH
HOH
3151
H
HOH
3152
6
HOH
HOH
3152
H
HOH
3154
6
HOH
HOH
3154
H
HOH
3156
6
HOH
HOH
3156
H
HOH
3157
6
HOH
HOH
3157
H
HOH
3159
6
HOH
HOH
3159
H
HOH
3160
6
HOH
HOH
3160
H
HOH
3161
6
HOH
HOH
3161
H
HOH
3162
6
HOH
HOH
3162
H
HOH
3164
6
HOH
HOH
3164
H
HOH
3165
6
HOH
HOH
3165
H
HOH
3166
6
HOH
HOH
3166
H
HOH
3167
6
HOH
HOH
3167
H
HOH
3169
6
HOH
HOH
3169
H
HOH
3170
6
HOH
HOH
3170
H
HOH
3171
6
HOH
HOH
3171
H
HOH
3172
6
HOH
HOH
3172
H
HOH
3174
6
HOH
HOH
3174
H
HOH
3176
6
HOH
HOH
3176
H
HOH
3177
6
HOH
HOH
3177
H
HOH
3178
6
HOH
HOH
3178
H
HOH
3179
6
HOH
HOH
3179
H
HOH
3180
6
HOH
HOH
3180
H
HOH
3181
6
HOH
HOH
3181
H
HOH
3182
6
HOH
HOH
3182
H
HOH
3183
6
HOH
HOH
3183
H
HOH
3184
6
HOH
HOH
3184
H
HOH
3185
6
HOH
HOH
3185
H
HOH
3186
6
HOH
HOH
3186
H
HOH
3187
6
HOH
HOH
3187
H
HOH
3189
6
HOH
HOH
3189
H
HOH
3190
6
HOH
HOH
3190
H
HOH
3191
6
HOH
HOH
3191
H
HOH
3193
6
HOH
HOH
3193
H
HOH
3194
6
HOH
HOH
3194
H
HOH
3195
6
HOH
HOH
3195
H
HOH
3112
6
HOH
HOH
3112
I
HOH
3158
6
HOH
HOH
3158
I
HOH
3163
6
HOH
HOH
3163
I
n
1
H
1
L
n
2
G
1
L
n
3
F
1
L
n
4
E
1
L
n
5
D
1
L
n
6
C
1
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
L
14
L
n
35
M
14
L
n
36
N
14
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
ARG
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
LYS
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
147
H
n
148
148
H
n
149
149
H
n
150
A
149
H
n
151
B
149
H
n
152
C
149
H
n
153
D
149
H
n
154
E
149
H
ALA
150
n
155
GLY
150
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
ALA
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
ALA
54
n
1
GLY
54
I
ALA
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
GLU
62
n
9
GLU
62
I
TYS
63
n
10
TYS
63
I
n
11
64
I
0.1840
0.1938
0.1775
0.1870
0.2363
0.250
1463
1706
5.0
4.9
29491
author_defined_assembly
3
trimeric
0
0
2700
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
3011
H
HOH
A
1
L
CG
LYS
14
A
CG
LYS
23
1
Y
A
1
L
CD
LYS
14
A
CD
LYS
23
1
Y
A
1
L
CE
LYS
14
A
CE
LYS
23
1
Y
A
1
L
NZ
LYS
14
A
NZ
LYS
23
1
Y
D
1
L
CG
ARG
14
A
CG
ARG
26
1
Y
D
1
L
CD
ARG
14
A
CD
ARG
26
1
Y
D
1
L
NE
ARG
14
A
NE
ARG
26
1
Y
D
1
L
CZ
ARG
14
A
CZ
ARG
26
1
Y
D
1
L
NH1
ARG
14
A
NH1
ARG
26
1
Y
D
1
L
NH2
ARG
14
A
NH2
ARG
26
1
Y
A
1
H
OG
SER
36
B
OG
SER
22
1
Y
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
109
B
CG
LYS
106
1
Y
1
H
CD
LYS
109
B
CD
LYS
106
1
Y
1
H
CE
LYS
109
B
CE
LYS
106
1
Y
1
H
NZ
LYS
109
B
NZ
LYS
106
1
Y
1
H
CG
LYS
110
B
CG
LYS
107
1
Y
1
H
CD
LYS
110
B
CD
LYS
107
1
Y
1
H
CE
LYS
110
B
CE
LYS
107
1
Y
1
H
NZ
LYS
110
B
NZ
LYS
107
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
GLU
192
B
CG
GLU
202
1
Y
1
H
CD
GLU
192
B
CD
GLU
202
1
Y
1
H
OE1
GLU
192
B
OE1
GLU
202
1
Y
1
H
OE2
GLU
192
B
OE2
GLU
202
1
Y
1
I
CG
ASP
55
C
CG
ASP
2
1
Y
1
I
OD1
ASP
55
C
OD1
ASP
2
1
Y
1
I
OD2
ASP
55
C
OD2
ASP
2
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
H
1
L
THR
1
A
THR
1
1
Y
G
1
L
PHE
1
A
PHE
2
1
Y
F
1
L
GLY
1
A
GLY
3
1
Y
E
1
L
SER
1
A
SER
4
1
Y
D
1
L
GLY
1
A
GLY
5
1
Y
C
1
L
GLU
1
A
GLU
6
1
Y
L
1
L
ASP
14
A
ASP
34
1
Y
M
1
L
GLY
14
A
GLY
35
1
Y
N
1
L
ARG
14
A
ARG
36
1
Y
1
H
THR
147
B
THR
147
1
Y
1
H
TRP
148
B
TRP
148
1
Y
1
H
THR
149
B
THR
149
1
Y
A
1
H
ALA
149
B
ALA
150
1
Y
B
1
H
ASN
149
B
ASN
151
1
Y
C
1
H
VAL
149
B
VAL
152
1
Y
D
1
H
GLY
149
B
GLY
153
1
Y
E
1
H
LYS
149
B
LYS
154
1
Y
1
H
GLU
247
B
GLU
259
1
Y
1
I
LEU
64
C
LEU
11
1
Y
1
3.62
0.50
120.30
123.92
L
L
L
NE
CZ
NH1
ARG
ARG
ARG
4
4
4
N
1
3.60
0.50
120.30
123.90
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
101
101
101
N
1
-3.39
0.50
120.30
116.91
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
206
206
206
N
1
L
PHE
7
-133.27
-89.89
1
H
GLN
38
-56.72
98.33
1
H
SER
48
-170.01
-173.84
A
1
H
TYR
60
-151.10
80.08
G
1
H
ASN
60
-152.72
78.01
1
H
HIS
71
-129.11
-65.42
1
H
ILE
79
-129.76
-62.57
ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
0.2500
0.1870
0.1938
0.1938
1.70
10.00
10137
1706
34569
34569
9639
4.9
90.2
RANDOM
1
FREE R
0.0
MOLECULAR REPLACEMENT
PDB entry 1H8D
ENGH & HUBER
3
0.00
2516.00
1.70
10.00
195
2514
37
0
2282
0.008
0.025
0.000
0.0262
0.044
0.054
0.011
0.000
0.076
0.000
1.7
20
2ZO3
37640
37640
0.029
1
26.7
2.9
97.8
1.70
1.73
2.55
1873
0.235
1
2.8
96.7
model building
SHELX
refinement
SHELXL-97
data collection
MAR345
data reduction
HKL-2000
data scaling
HKL-2000
phasing
CNS
Bisphenylic Thrombin Inhibitors
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
5
N
N
6
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
CYS
58
B
CYS
44
5
3
4
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
2.040
L
CYS
1
A
SG
CYS
9
1_555
H
CYS
122
B
SG
CYS
119
1_555
disulf
2.025
H
CYS
42
B
SG
CYS
28
1_555
H
CYS
58
B
SG
CYS
44
1_555
disulf
2.023
H
CYS
168
B
SG
CYS
173
1_555
H
CYS
182
B
SG
CYS
187
1_555
disulf
2.000
H
CYS
191
B
SG
CYS
201
1_555
H
CYS
220
B
SG
CYS
231
1_555
covale
1.338
both
I
GLU
62
C
C
GLU
9
1_555
I
TYS
63
C
N
TYS
10
1_555
Hydrolase/Hydrolase Inhibitor
Blood Clotting, Hydrolase Inhibitor, Acute phase, Blood coagulation, Cleavage on pair of basic residues, Gamma-carboxyglutamic acid, Glycoprotein, Kringle, Secreted, Serine protease, Hydrolase-Hydrolase Inhibitor complex
H
SER
36
B
SER
22
A
1
H
PRO
37
B
PRO
23
-3.01
THRB_HUMAN
UNP
1
328
P00734
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
THRB_HUMAN
UNP
2
364
P00734
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISM
LEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL
QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE
ITH1_HIRME
UNP
3
54
P01050
GDFEEIPEEYL
328
363
2ZO3
1
14
P00734
H
N
L
1
1
36
364
622
2ZO3
16
247
P00734
H
2
1
259
54
64
2ZO3
54
64
P01050
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 33U H 2501
H
33U
2501
Software
19
BINDING SITE FOR RESIDUE NA H 2502
H
NA
2502
Software
6
BINDING SITE FOR RESIDUE NA H 2503
H
NA
2503
Software
6
BINDING SITE FOR CHAIN I OF HIRUDIN VARIANT-1
Software
15
H
HIS
57
B
HIS
43
19
1_555
H
TYR
60
B
TYR
47
A
19
1_555
H
GLU
97
B
GLU
94
A
19
1_555
H
LEU
99
B
LEU
96
19
1_555
H
ILE
174
B
ILE
179
19
1_555
H
ASP
189
B
ASP
199
19
1_555
H
ALA
190
B
ALA
200
19
1_555
H
SER
195
B
SER
205
19
1_555
H
VAL
213
B
VAL
225
19
1_555
H
SER
214
B
SER
226
19
1_555
H
TRP
215
B
TRP
227
19
1_555
H
GLY
216
B
GLY
228
19
1_555
H
GLU
217
B
GLU
229
19
1_555
H
GLY
219
B
GLY
230
19
1_555
H
GLY
226
B
GLY
238
19
1_555
H
HOH
3005
H
HOH
19
1_555
H
HOH
3122
H
HOH
19
1_555
H
HOH
3167
H
HOH
19
1_555
H
HOH
3179
H
HOH
19
1_555
H
ARG
221
B
ARG
233
A
6
1_555
H
LYS
224
B
LYS
236
6
1_555
H
HOH
3034
H
HOH
6
1_555
H
HOH
3061
H
HOH
6
1_555
H
HOH
3079
H
HOH
6
1_555
H
HOH
3177
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
3023
H
HOH
6
1_555
H
HOH
3042
H
HOH
6
1_555
H
HOH
3047
H
HOH
6
1_555
H
PHE
34
B
PHE
19
15
1_555
H
GLN
38
B
GLN
24
15
1_555
H
LEU
40
B
LEU
26
15
1_555
H
LEU
65
B
LEU
60
15
1_555
H
ARG
73
B
ARG
68
15
1_555
H
THR
74
B
THR
69
15
1_555
H
ARG
75
B
ARG
70
15
1_555
H
TYR
76
B
TYR
71
15
1_555
H
LYS
81
B
LYS
77
15
1_555
H
ILE
82
B
ILE
78
15
1_555
H
HOH
3050
H
HOH
15
1_555
H
HOH
3086
H
HOH
15
1_555
I
HOH
3112
I
HOH
15
1_555
I
HOH
3158
I
HOH
15
1_555
I
HOH
3163
I
HOH
15
1_555
5
C 1 2 1