0.011293
0.000000
0.000000
0.000000
0.011293
0.000000
0.000000
0.000000
0.009710
0.00000
0.00000
0.00000
RESIDUE PRO H 37 IS A CIS PROLINE.
Bode, W.
Brandstetter, H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
88.550
88.550
102.990
C22 H28 N4 O3 S
428.548
4-[(2S)-2-{[(4-methylphenyl)sulfonyl]amino}-3-oxo-3-(piperidin-1-yl)propyl]benzene-1-carboximidamide
non-polymer
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
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
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
226
1085
1099
10.1016/0022-2836(92)91054-S
1518046
Refined 2.3 A X-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors NAPAP, 4-TAPAP and MQPA. A starting point for improving antithrombotics.
1992
To be Published
0353
Crystallographic Determination of Thrombin Complexes with Small Synthetic Inhibitors as a Starting Point for the Receptor-Based Design of Antithrombotics
To be Published
0353
X-Ray Crystal Structure of Thrombin in Complex with D-Phe-Pro-Arg and with Small Benzamidine and Arginine-Based "Non-Peptidic" Inhibitors
US
Protein Sci.
PRCIEI
0795
0961-8368
1
426
The Refined 1.9-Angstroms X-Ray Crystal Structure of D-Phe-Pro-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, Detailed Active-Site Geometry, and Structure-Function Relationships
1992
NE
FEBS Lett.
FEBLAL
0165
0014-5793
287
133
Geometry of Binding of the Nalpha-Tosylated Piperidides of M-Amidino-, P-Amidino-and P-Guanidino Phenylalanine to Thrombin and Trypsin: X-Ray Crystal Structures of Their Trypsin Complexes and Modeling of Their Thrombin Complexes
1991
IX
Eur.J.Biochem.
EJBCAI
0262
0014-2956
193
175
Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N-Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophenylalanyl-Piperidine (Napap) and (2R,4R)-4-Methyl-1-[N-Alpha-(3-Methyl-1,2,3,4-Tetrahydro-8-Quinolinesulphonyl)-L-Arginyl]-2-Piperidine Carboxylic Acid (Mqpa) to Human Alpha-Thrombin: X-Ray Crystallographic Determination of the Napap-Trypsin Complex and Modeling of Napap-Thrombin and Mqpa-Thrombin
1990
UK
Embo J.
EMJODG
0897
0261-4189
8
3467
The Refined 1.9 Angstroms Crystal Structure of Human Alpha-Thrombin: Interaction with D-Phe-Pro-Arg Chloromethylketone and Significance of the Tyr-Pro-Pro-Trp Insertion Segment
1989
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
5735.240
EPSILON-THROMBIN
3.4.21.5
1
man
polymer
29772.422
EPSILON-THROMBIN
3.4.21.5
1
man
polymer
428.548
4-[(2S)-2-{[(4-methylphenyl)sulfonyl]amino}-3-oxo-3-(piperidin-1-yl)propyl]benzene-1-carboximidamide
1
syn
non-polymer
18.015
water
180
nat
water
no
no
TSEDHFQPFFNEKTFGAGEADCGLRPLFEKKQVQDQTEKELFESYIEGR
TSEDHFQPFFNEKTFGAGEADCGLRPLFEKKQVQDQTEKELFESYIEGR
L
polypeptide(L)
no
no
IVEGQDAEVGLSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTVDDLLVRIGKHSRTRYERKVEKISM
LDKIYIHPRYNWKENLDRDIALLKLKRPIELSDYIHPVCLPDKQTAAKLLHAGFKGRVTGWGNRRETWTTSVAEVQPSVL
QVVNLPLVERPVCKASTRIRITDNMFCAGYKPGEGKRGDACEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDRLGS
IVEGQDAEVGLSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTVDDLLVRIGKHSRTRYERKVEKISM
LDKIYIHPRYNWKENLDRDIALLKLKRPIELSDYIHPVCLPDKQTAAKLLHAGFKGRVTGWGNRRETWTTSVAEVQPSVL
QVVNLPLVERPVCKASTRIRITDNMFCAGYKPGEGKRGDACEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDRLGS
H
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
n
n
cow
sample
9913
Bos taurus
cow
sample
9913
Bos taurus
2.84
56.71
pdbx_database_status
pdbx_molecule_features
pdbx_unobs_or_zero_occ_residues
repository
Initial release
Version format compliance
Atomic model
Database references
Derived calculations
Non-polymer description
Structure summary
Version format compliance
Other
Non-polymer description
Advisory
Data collection
Other
Structure summary
1
0
1994-01-31
1
1
2008-03-24
1
2
2011-07-13
1
3
2012-12-12
1
4
2016-12-14
1
5
2018-09-12
_pdbx_database_status.process_site
SHEET
THE SHEETS PRESENTED AS *S1* AND *S2* ON SHEET RECORDS
BELOW ARE ACTUALLY SIX-STRANDED BETA-BARRELS. THESE ARE
REPRESENTED BY SEVEN-STRANDED SHEETS IN WHICH THE FIRST AND
LAST STRANDS ARE IDENTICAL.
Y
BNL
1992-07-06
REL
4QQ
4-[(2S)-2-{[(4-methylphenyl)sulfonyl]amino}-3-oxo-3-(piperidin-1-yl)propyl]benzene-1-carboximidamide
HOH
water
AMIDINOPHENYLALANINE (OF 4-TAPAP) BINDS TO S1
SPECIFICITY POCKET, PIPERIDINE TO S2 AND TOLMENE
GROUP TO "ARYL BINDING SITE".
THE NUMBERING OF THROMBIN RESIDUES IS BASED ON TOPOLOGICAL
EQUIVALENCES WITH CHYMOTRYPSINOGEN.
TOS
1
3
4QQ
4QQ
301
H
HOH
279
4
HOH
HOH
101
L
HOH
284
4
HOH
HOH
102
L
HOH
286
4
HOH
HOH
103
L
HOH
289
4
HOH
HOH
104
L
HOH
291
4
HOH
HOH
105
L
HOH
293
4
HOH
HOH
106
L
HOH
297
4
HOH
HOH
107
L
HOH
301
4
HOH
HOH
108
L
HOH
304
4
HOH
HOH
109
L
HOH
311
4
HOH
HOH
110
L
HOH
324
4
HOH
HOH
111
L
HOH
330
4
HOH
HOH
112
L
HOH
334
4
HOH
HOH
113
L
HOH
342
4
HOH
HOH
114
L
HOH
350
4
HOH
HOH
115
L
HOH
363
4
HOH
HOH
116
L
HOH
365
4
HOH
HOH
117
L
HOH
372
4
HOH
HOH
118
L
HOH
395
4
HOH
HOH
119
L
HOH
396
4
HOH
HOH
120
L
HOH
426
4
HOH
HOH
121
L
HOH
276
4
HOH
HOH
401
H
HOH
277
4
HOH
HOH
402
H
HOH
278
4
HOH
HOH
403
H
HOH
280
4
HOH
HOH
404
H
HOH
281
4
HOH
HOH
405
H
HOH
282
4
HOH
HOH
406
H
HOH
283
4
HOH
HOH
407
H
HOH
285
4
HOH
HOH
408
H
HOH
287
4
HOH
HOH
409
H
HOH
290
4
HOH
HOH
410
H
HOH
292
4
HOH
HOH
411
H
HOH
295
4
HOH
HOH
412
H
HOH
298
4
HOH
HOH
413
H
HOH
299
4
HOH
HOH
414
H
HOH
300
4
HOH
HOH
415
H
HOH
303
4
HOH
HOH
416
H
HOH
305
4
HOH
HOH
417
H
HOH
306
4
HOH
HOH
418
H
HOH
307
4
HOH
HOH
419
H
HOH
309
4
HOH
HOH
420
H
HOH
310
4
HOH
HOH
421
H
HOH
313
4
HOH
HOH
422
H
HOH
315
4
HOH
HOH
423
H
HOH
316
4
HOH
HOH
424
H
HOH
317
4
HOH
HOH
425
H
HOH
318
4
HOH
HOH
426
H
HOH
321
4
HOH
HOH
427
H
HOH
322
4
HOH
HOH
428
H
HOH
325
4
HOH
HOH
429
H
HOH
327
4
HOH
HOH
430
H
HOH
331
4
HOH
HOH
431
H
HOH
332
4
HOH
HOH
432
H
HOH
335
4
HOH
HOH
433
H
HOH
336
4
HOH
HOH
434
H
HOH
337
4
HOH
HOH
435
H
HOH
339
4
HOH
HOH
436
H
HOH
340
4
HOH
HOH
437
H
HOH
341
4
HOH
HOH
438
H
HOH
345
4
HOH
HOH
439
H
HOH
347
4
HOH
HOH
440
H
HOH
348
4
HOH
HOH
441
H
HOH
349
4
HOH
HOH
442
H
HOH
351
4
HOH
HOH
443
H
HOH
352
4
HOH
HOH
444
H
HOH
353
4
HOH
HOH
445
H
HOH
356
4
HOH
HOH
446
H
HOH
359
4
HOH
HOH
447
H
HOH
360
4
HOH
HOH
448
H
HOH
361
4
HOH
HOH
449
H
HOH
364
4
HOH
HOH
450
H
HOH
367
4
HOH
HOH
451
H
HOH
373
4
HOH
HOH
452
H
HOH
374
4
HOH
HOH
453
H
HOH
376
4
HOH
HOH
454
H
HOH
377
4
HOH
HOH
455
H
HOH
380
4
HOH
HOH
456
H
HOH
382
4
HOH
HOH
457
H
HOH
386
4
HOH
HOH
458
H
HOH
391
4
HOH
HOH
459
H
HOH
392
4
HOH
HOH
460
H
HOH
401
4
HOH
HOH
461
H
HOH
402
4
HOH
HOH
462
H
HOH
405
4
HOH
HOH
463
H
HOH
409
4
HOH
HOH
464
H
HOH
416
4
HOH
HOH
465
H
HOH
417
4
HOH
HOH
466
H
HOH
418
4
HOH
HOH
467
H
HOH
423
4
HOH
HOH
468
H
HOH
424
4
HOH
HOH
469
H
HOH
425
4
HOH
HOH
470
H
HOH
433
4
HOH
HOH
471
H
HOH
434
4
HOH
HOH
472
H
HOH
435
4
HOH
HOH
473
H
HOH
438
4
HOH
HOH
474
H
HOH
439
4
HOH
HOH
475
H
HOH
440
4
HOH
HOH
476
H
HOH
446
4
HOH
HOH
477
H
HOH
447
4
HOH
HOH
478
H
HOH
449
4
HOH
HOH
479
H
HOH
451
4
HOH
HOH
480
H
HOH
452
4
HOH
HOH
481
H
HOH
456
4
HOH
HOH
482
H
HOH
457
4
HOH
HOH
483
H
HOH
458
4
HOH
HOH
484
H
HOH
461
4
HOH
HOH
485
H
HOH
462
4
HOH
HOH
486
H
HOH
466
4
HOH
HOH
487
H
HOH
467
4
HOH
HOH
488
H
HOH
470
4
HOH
HOH
489
H
HOH
471
4
HOH
HOH
490
H
HOH
473
4
HOH
HOH
491
H
HOH
477
4
HOH
HOH
492
H
HOH
480
4
HOH
HOH
493
H
HOH
481
4
HOH
HOH
494
H
HOH
483
4
HOH
HOH
495
H
HOH
486
4
HOH
HOH
496
H
HOH
490
4
HOH
HOH
497
H
HOH
492
4
HOH
HOH
498
H
HOH
495
4
HOH
HOH
499
H
HOH
499
4
HOH
HOH
500
H
HOH
500
4
HOH
HOH
501
H
HOH
503
4
HOH
HOH
502
H
HOH
504
4
HOH
HOH
503
H
HOH
505
4
HOH
HOH
504
H
HOH
506
4
HOH
HOH
505
H
HOH
507
4
HOH
HOH
506
H
HOH
508
4
HOH
HOH
507
H
HOH
509
4
HOH
HOH
508
H
HOH
510
4
HOH
HOH
509
H
HOH
511
4
HOH
HOH
510
H
HOH
512
4
HOH
HOH
511
H
HOH
516
4
HOH
HOH
512
H
HOH
518
4
HOH
HOH
513
H
HOH
520
4
HOH
HOH
514
H
HOH
521
4
HOH
HOH
515
H
HOH
526
4
HOH
HOH
516
H
HOH
527
4
HOH
HOH
517
H
HOH
528
4
HOH
HOH
518
H
HOH
529
4
HOH
HOH
519
H
HOH
530
4
HOH
HOH
520
H
HOH
535
4
HOH
HOH
521
H
HOH
536
4
HOH
HOH
522
H
HOH
539
4
HOH
HOH
523
H
HOH
542
4
HOH
HOH
524
H
HOH
544
4
HOH
HOH
525
H
HOH
545
4
HOH
HOH
526
H
HOH
546
4
HOH
HOH
527
H
HOH
547
4
HOH
HOH
528
H
HOH
551
4
HOH
HOH
529
H
HOH
556
4
HOH
HOH
530
H
HOH
557
4
HOH
HOH
531
H
HOH
559
4
HOH
HOH
532
H
HOH
560
4
HOH
HOH
533
H
HOH
562
4
HOH
HOH
534
H
HOH
563
4
HOH
HOH
535
H
HOH
564
4
HOH
HOH
536
H
HOH
565
4
HOH
HOH
537
H
HOH
566
4
HOH
HOH
538
H
HOH
567
4
HOH
HOH
539
H
HOH
568
4
HOH
HOH
540
H
HOH
569
4
HOH
HOH
541
H
HOH
570
4
HOH
HOH
542
H
HOH
572
4
HOH
HOH
543
H
HOH
577
4
HOH
HOH
544
H
HOH
578
4
HOH
HOH
545
H
HOH
579
4
HOH
HOH
546
H
HOH
580
4
HOH
HOH
547
H
HOH
582
4
HOH
HOH
548
H
HOH
584
4
HOH
HOH
549
H
HOH
585
4
HOH
HOH
550
H
HOH
590
4
HOH
HOH
551
H
HOH
591
4
HOH
HOH
552
H
HOH
594
4
HOH
HOH
553
H
HOH
596
4
HOH
HOH
554
H
HOH
600
4
HOH
HOH
555
H
HOH
601
4
HOH
HOH
556
H
HOH
605
4
HOH
HOH
557
H
HOH
606
4
HOH
HOH
558
H
HOH
608
4
HOH
HOH
559
H
n
1
-12
L
n
2
-11
L
n
3
-10
L
n
4
-9
L
n
5
-8
L
n
6
-7
L
n
7
-6
L
n
8
-5
L
n
9
-4
L
n
10
-3
L
n
11
-2
L
n
12
-1
L
n
13
0
L
THR
1
n
14
H
THR
1
L
PHE
1
n
15
G
PHE
1
L
GLY
1
n
16
F
GLY
1
L
ALA
1
n
17
E
ALA
1
L
GLY
1
n
18
D
GLY
1
L
GLU
1
n
19
C
GLU
1
L
ALA
1
n
20
B
ALA
1
L
ASP
1
n
21
A
ASP
1
L
CYS
1
n
22
CYS
1
L
GLY
2
n
23
GLY
2
L
LEU
3
n
24
LEU
3
L
ARG
4
n
25
ARG
4
L
PRO
5
n
26
PRO
5
L
LEU
6
n
27
LEU
6
L
PHE
7
n
28
PHE
7
L
GLU
8
n
29
GLU
8
L
LYS
9
n
30
LYS
9
L
LYS
10
n
31
LYS
10
L
GLN
11
n
32
GLN
11
L
VAL
12
n
33
VAL
12
L
GLN
13
n
34
GLN
13
L
ASP
14
n
35
ASP
14
L
GLN
14
n
36
A
GLN
14
L
THR
14
n
37
B
THR
14
L
GLU
14
n
38
C
GLU
14
L
LYS
14
n
39
D
LYS
14
L
GLU
14
n
40
E
GLU
14
L
LEU
14
n
41
F
LEU
14
L
PHE
14
n
42
G
PHE
14
L
GLU
14
n
43
H
GLU
14
L
SER
14
n
44
I
SER
14
L
TYR
14
n
45
J
TYR
14
L
ILE
14
n
46
K
ILE
14
L
GLU
14
n
47
L
GLU
14
L
GLY
14
n
48
M
GLY
14
L
ARG
15
n
49
ARG
15
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
GLN
20
n
5
GLN
20
H
ASP
21
n
6
ASP
21
H
ALA
22
n
7
ALA
22
H
GLU
23
n
8
GLU
23
H
VAL
24
n
9
VAL
24
H
GLY
25
n
10
GLY
25
H
LEU
26
n
11
LEU
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
VAL
61
n
56
VAL
61
H
ASP
62
n
57
ASP
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
ARG
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
LYS
78
n
74
LYS
78
H
VAL
79
n
75
VAL
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
ASP
86
n
82
ASP
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
LYS
97
n
93
LYS
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
LEU
106
n
103
LEU
106
H
LYS
107
n
104
LYS
107
H
LEU
108
n
105
LEU
108
H
LYS
109
n
106
LYS
109
H
ARG
110
n
107
ARG
110
H
PRO
111
n
108
PRO
111
H
ILE
112
n
109
ILE
112
H
GLU
113
n
110
GLU
113
H
LEU
114
n
111
LEU
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
LYS
126
n
123
LYS
126
H
GLN
127
n
124
GLN
127
H
THR
128
n
125
THR
128
H
ALA
129
n
126
ALA
129
H
ALA
129
n
127
A
ALA
129
H
LYS
129
n
128
B
LYS
129
H
LEU
129
n
129
C
LEU
129
H
LEU
130
n
130
LEU
130
H
HIS
131
n
131
HIS
131
H
ALA
132
n
132
ALA
132
H
GLY
133
n
133
GLY
133
H
PHE
134
n
134
PHE
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
ARG
144
n
144
ARG
144
H
ARG
145
n
145
ARG
145
H
GLU
146
n
146
GLU
146
H
THR
147
n
147
THR
147
H
TRP
148
n
148
TRP
148
H
THR
149
n
149
THR
149
H
THR
149
n
150
A
THR
149
H
SER
149
n
151
B
SER
149
H
VAL
149
n
152
C
VAL
149
H
ALA
149
n
153
D
ALA
149
H
GLU
149
n
154
E
GLU
149
H
VAL
150
n
155
VAL
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
LEU
162
n
167
LEU
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
ALA
170
n
175
ALA
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
GLY
186
n
193
A
GLY
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
TYR
204
n
215
A
TYR
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
A
ASP
221
H
ARG
221
n
233
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
ARG
244
n
256
ARG
244
H
LEU
245
n
257
LEU
245
H
GLY
246
n
258
GLY
246
H
SER
247
n
259
SER
247
H
author_and_software_defined_assembly
PISA
2
dimeric
2670
-13
13940
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
1
L
THR
-12
A
THR
1
1
Y
1
L
SER
-11
A
SER
2
1
Y
1
L
GLU
-10
A
GLU
3
1
Y
1
L
ASP
-9
A
ASP
4
1
Y
1
L
HIS
-8
A
HIS
5
1
Y
1
L
PHE
-7
A
PHE
6
1
Y
1
L
GLN
-6
A
GLN
7
1
Y
1
L
PRO
-5
A
PRO
8
1
Y
1
L
PHE
-4
A
PHE
9
1
Y
1
L
PHE
-3
A
PHE
10
1
Y
1
L
ASN
-2
A
ASN
11
1
Y
1
L
GLU
-1
A
GLU
12
1
Y
1
L
LYS
0
A
LYS
13
1
Y
1
H
H
ALA
GLU
22
23
148.91
1
H
H
ARG
PRO
110
111
144.78
E
1
H
H
GLU
VAL
149
150
-147.55
1
H
H
PRO
SER
152
153
142.07
1
H
H
PRO
VAL
166
167
144.04
1
H
H
ARG
ILE
173
174
-149.41
A
B
1
H
H
GLY
GLU
186
186
-147.36
1
H
H
ASP
ALA
189
190
147.04
1
H
H
GLY
SER
246
247
128.91
1
H
ARG
101
0.091
SIDE CHAIN
A
1
H
TYR
184
0.124
SIDE CHAIN
A
1
H
TYR
204
0.069
SIDE CHAIN
1
10.37
1.10
114.20
124.57
L
L
L
CA
CB
SG
CYS
CYS
CYS
1
1
1
N
1
5.92
0.80
106.30
112.22
H
H
H
CD1
CG
CD2
TRP
TRP
TRP
29
29
29
N
1
-6.01
0.80
107.30
101.29
H
H
H
CE2
CD2
CG
TRP
TRP
TRP
29
29
29
N
1
7.33
0.80
106.30
113.63
H
H
H
CD1
CG
CD2
TRP
TRP
TRP
51
51
51
N
1
-6.04
0.80
107.30
101.26
H
H
H
CE2
CD2
CG
TRP
TRP
TRP
51
51
51
N
D
D
D
1
5.75
0.80
106.30
112.05
H
H
H
CD1
CG
CD2
TRP
TRP
TRP
60
60
60
N
D
D
D
1
-5.13
0.80
107.30
102.17
H
H
H
CE2
CD2
CG
TRP
TRP
TRP
60
60
60
N
1
-3.66
0.60
121.00
117.34
H
H
H
CB
CG
CD1
TYR
TYR
TYR
76
76
76
N
1
6.95
0.80
106.30
113.25
H
H
H
CD1
CG
CD2
TRP
TRP
TRP
96
96
96
N
1
-5.97
0.80
107.30
101.33
H
H
H
CE2
CD2
CG
TRP
TRP
TRP
96
96
96
N
1
-3.34
0.50
120.30
116.96
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
101
101
101
N
1
8.41
0.80
106.30
114.71
H
H
H
CD1
CG
CD2
TRP
TRP
TRP
141
141
141
N
1
-6.82
1.00
110.10
103.28
H
H
H
CG
CD1
NE1
TRP
TRP
TRP
141
141
141
N
1
-6.19
0.80
107.30
101.11
H
H
H
CE2
CD2
CG
TRP
TRP
TRP
141
141
141
N
1
3.97
0.50
120.30
124.27
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
145
145
145
N
1
6.42
0.80
106.30
112.72
H
H
H
CD1
CG
CD2
TRP
TRP
TRP
148
148
148
N
1
-5.91
0.80
107.30
101.39
H
H
H
CE2
CD2
CG
TRP
TRP
TRP
148
148
148
N
1
18.10
2.20
113.40
131.50
H
H
H
CA
CB
CG
GLU
GLU
GLU
164
164
164
N
1
7.03
1.10
114.20
121.23
H
H
H
CA
CB
SG
CYS
CYS
CYS
182
182
182
N
A
A
A
1
-4.74
0.60
121.00
116.26
H
H
H
CB
CG
CD2
TYR
TYR
TYR
184
184
184
N
1
15.71
2.60
112.10
127.81
H
H
H
N
CA
C
PRO
PRO
PRO
186
186
186
N
1
-12.85
1.20
123.30
110.45
H
H
H
OE1
CD
OE2
GLU
GLU
GLU
192
192
192
N
1
19.09
2.00
118.30
137.39
H
H
H
CG
CD
OE1
GLU
GLU
GLU
192
192
192
N
A
A
A
1
-4.09
0.60
121.00
116.91
H
H
H
CB
CG
CD1
TYR
TYR
TYR
204
204
204
N
1
6.53
0.80
106.30
112.83
H
H
H
CD1
CG
CD2
TRP
TRP
TRP
207
207
207
N
1
-5.24
0.80
107.30
102.06
H
H
H
CE2
CD2
CG
TRP
TRP
TRP
207
207
207
N
1
5.72
0.90
133.90
139.62
H
H
H
CG
CD2
CE3
TRP
TRP
TRP
207
207
207
N
1
5.14
0.80
106.30
111.44
H
H
H
CD1
CG
CD2
TRP
TRP
TRP
215
215
215
N
1
-5.52
0.80
107.30
101.78
H
H
H
CE2
CD2
CG
TRP
TRP
TRP
215
215
215
N
1
6.39
0.80
106.30
112.69
H
H
H
CD1
CG
CD2
TRP
TRP
TRP
237
237
237
N
1
-5.70
0.80
107.30
101.60
H
H
H
CE2
CD2
CG
TRP
TRP
TRP
237
237
237
N
1
H
H
NE2
CD2
HIS
HIS
57
57
-0.068
0.011
1.373
1.305
N
1
H
H
NE2
CD2
HIS
HIS
91
91
-0.070
0.011
1.373
1.303
N
1
H
H
NE2
CD2
HIS
HIS
119
119
-0.066
0.011
1.373
1.307
N
1
H
H
NE2
CD2
HIS
HIS
131
131
-0.072
0.011
1.373
1.301
N
1
H
H
CD
OE2
GLU
GLU
192
192
-0.161
0.011
1.252
1.091
N
1
H
H
NE2
CD2
HIS
HIS
230
230
-0.067
0.011
1.373
1.306
N
E
1
L
ALA
1
66.74
-62.82
C
1
L
GLU
1
-70.61
24.01
B
1
L
ALA
1
50.46
-64.03
1
L
PHE
7
-133.10
-72.34
A
1
H
SER
36
-174.53
125.73
1
H
ASP
49
-66.25
15.98
1
H
ARG
50
-149.69
-39.82
C
1
H
PRO
60
-39.43
-29.94
E
1
H
ASP
60
43.18
23.68
1
H
ASP
62
-88.17
49.65
1
H
ASP
63
-143.54
-11.00
1
H
HIS
71
-164.47
-49.81
1
H
TYR
76
-36.37
95.98
1
H
LYS
97
-90.18
48.78
A
1
H
GLU
97
179.46
-83.26
1
H
ASN
98
-140.18
14.78
1
H
ASP
102
-67.03
76.71
1
H
ASN
143
-22.36
129.97
1
H
TRP
148
-87.83
-114.86
A
1
H
THR
149
-122.02
-131.99
D
1
H
ALA
149
-102.45
-109.45
E
1
H
GLU
149
-178.37
-10.20
1
H
SER
153
-20.19
-66.22
1
H
LEU
155
-38.32
132.52
1
H
PRO
166
-50.31
-72.60
1
H
VAL
167
-30.91
-29.55
1
H
ASP
178
-56.04
-9.43
1
H
PRO
186
-23.20
-40.05
B
1
H
GLU
186
-69.13
23.37
1
H
CYS
191
179.29
172.31
1
H
SER
214
-93.78
-78.92
A
1
H
ASP
221
66.36
65.21
1
H
HIS
230
-67.05
90.13
1
H
ARG
244
84.09
-32.03
THERE IS A CLEAVAGE IN THE CHAIN AT THR 149A - SER 149B IN
THE INSERTION LOOP OF THROMBIN. THE AUTHORS DO NOT SEE
THIS CLEAVAGE DUE TO DISORDER AT BOTH FLANKING REGIONS.
NOTE THAT THE OCCUPANCY OF RESIDUES 148 - 149E IS GIVEN AS
0.0 INDICATING THAT THEY WERE NOT SEEN IN THE ELECTRON
DENSITY MAPS.
0.167
0.167
2.5
8.0
1
2.5
8.0
180
2594
30
0
2384
0.013
3.366
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
EPSILON-THROMBIN (E.C.3.4.21.5) NON-COVALENT COMPLEX WITH 4-TAPAP
REFINED 2.3 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF BOVINE THROMBIN COMPLEXES FORMED WITH THE BENZAMIDINE AND ARGININE-BASED THROMBIN INHIBITORS NAPAP, 4-TAPAP AND MQPA: A STARTING POINT FOR IMPROVING ANTITHROMBOTICS
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
L
GLU
14
A
GLU
38
HELX_P
3.6/13
L
SER
14
A
SER
44
1
1
7
C
I
H
ALA
55
B
ALA
41
HELX_P
H
LEU
59
B
LEU
45
5
2
5
H
TYR
60
B
TYR
47
HELX_P
H
ASP
60
B
ASP
51
5
3
5
A
E
H
ASP
125
B
ASP
122
HELX_P
3.6/13
H
LEU
129
B
LEU
129
1
4
8
C
H
GLU
164
B
GLU
169
HELX_P
3.6/13
H
LYS
169
B
LYS
174
1
5
6
H
CYS
168
B
CYS
173
HELX_P
H
THR
172
B
THR
177
5
6
5
H
VAL
231
B
VAL
243
HELX_P
H
LYS
235
B
LYS
247
5
7
5
H
LEU
234
B
LEU
246
HELX_P
3.6/13
H
ASP
243
B
ASP
255
1
8
10
disulf
2.009
L
CYS
1
A
SG
CYS
22
1_555
H
CYS
122
B
SG
CYS
119
1_555
disulf
2.015
H
CYS
42
B
SG
CYS
28
1_555
H
CYS
58
B
SG
CYS
44
1_555
disulf
2.043
H
CYS
168
B
SG
CYS
173
1_555
H
CYS
182
B
SG
CYS
187
1_555
disulf
2.025
H
CYS
191
B
SG
CYS
201
1_555
H
CYS
220
B
SG
CYS
231
1_555
HYDROLASE/HYDROLASE inhibitor
SERINE PROTEINASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX
H
SER
36
B
SER
22
A
1
H
PRO
37
B
PRO
23
-14.23
THRB_BOVIN
UNP
1
1
P00735
MARVRGPRLPGCLALAALFSLVHSQHVFLAHQQASSLLQRARRANKGFLEEVRKGNLERECLEEPCSREEAFEALESLSA
TDAFWAKYTACESARNPREKLNECLEGNCAEGVGMNYRGNVSVTRSGIECQLWRSRYPHKPEINSTTHPGADLRENFCRN
PDGSITGPWCYTTSPTLRREECSVPVCGQDRVTVEVIPRSGGSTTSQSPLLETCVPDRGREYRGRLAVTTSGSRCLAWSS
EQAKALSKDQDFNPAVPLAENFCRNPDGDEEGAWCYVADQPGDFEYCDLNYCEEPVDGDLGDRLGEDPDPDAAIEGRTSE
DHFQPFFNEKTFGAGEADCGLRPLFEKKQVQDQTEKELFESYIEGRIVEGQDAEVGLSPWQVMLFRKSPQELLCGASLIS
DRWVLTAAHCLLYPPWDKNFTVDDLLVRIGKHSRTRYERKVEKISMLDKIYIHPRYNWKENLDRDIALLKLKRPIELSDY
IHPVCLPDKQTAAKLLHAGFKGRVTGWGNRRETWTTSVAEVQPSVLQVVNLPLVERPVCKASTRIRITDNMFCAGYKPGE
GKRGDACEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDRLGS
THRB_BOVIN
UNP
2
1
P00735
MARVRGPRLPGCLALAALFSLVHSQHVFLAHQQASSLLQRARRANKGFLEEVRKGNLERECLEEPCSREEAFEALESLSA
TDAFWAKYTACESARNPREKLNECLEGNCAEGVGMNYRGNVSVTRSGIECQLWRSRYPHKPEINSTTHPGADLRENFCRN
PDGSITGPWCYTTSPTLRREECSVPVCGQDRVTVEVIPRSGGSTTSQSPLLETCVPDRGREYRGRLAVTTSGSRCLAWSS
EQAKALSKDQDFNPAVPLAENFCRNPDGDEEGAWCYVADQPGDFEYCDLNYCEEPVDGDLGDRLGEDPDPDAAIEGRTSE
DHFQPFFNEKTFGAGEADCGLRPLFEKKQVQDQTEKELFESYIEGRIVEGQDAEVGLSPWQVMLFRKSPQELLCGASLIS
DRWVLTAAHCLLYPPWDKNFTVDDLLVRIGKHSRTRYERKVEKISMLDKIYIHPRYNWKENLDRDIALLKLKRPIELSDY
IHPVCLPDKQTAAKLLHAGFKGRVTGWGNRRETWTTSVAEVQPSVLQVVNLPLVERPVCKASTRIRITDNMFCAGYKPGE
GKRGDACEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDRLGS
318
366
1ETT
-12
15
P00735
L
1
1
49
367
625
1ETT
16
247
P00735
H
2
1
259
7
7
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
LYS
81
B
LYS
77
H
ASN
95
B
ASN
91
H
ASP
100
B
ASP
97
H
LYS
109
B
LYS
106
H
VAL
52
B
VAL
38
H
THR
54
B
THR
40
H
GLU
39
B
GLU
25
H
LEU
46
B
LEU
32
H
TRP
29
B
TRP
14
H
ARG
35
B
ARG
20
H
VAL
66
B
VAL
61
H
ILE
68
B
ILE
63
H
LYS
81
B
LYS
77
H
ASN
95
B
ASN
91
H
VAL
150
B
VAL
155
H
LEU
162
B
LEU
167
H
PHE
134
B
PHE
134
H
ARG
144
B
ARG
144
H
PHE
199
B
PHE
209
H
SER
203
B
SER
213
H
ARG
206
B
ARG
218
H
TRP
215
B
TRP
227
H
GLY
226
B
GLY
238
H
THR
229
B
THR
241
H
PHE
181
B
PHE
186
H
ALA
183
B
ALA
188
H
VAL
150
B
VAL
155
H
LEU
162
B
LEU
167
BINDING SITE FOR RESIDUE 4QQ H 301
Software
12
H
HIS
57
B
HIS
43
12
1_555
H
TYR
60
B
TYR
47
A
12
1_555
H
TRP
60
B
TRP
50
D
12
1_555
H
LEU
99
B
LEU
96
12
1_555
H
ASP
189
B
ASP
199
12
1_555
H
ALA
190
B
ALA
200
12
1_555
H
VAL
213
B
VAL
225
12
1_555
H
SER
214
B
SER
226
12
1_555
H
TRP
215
B
TRP
227
12
1_555
H
GLY
216
B
GLY
228
12
1_555
H
GLY
219
B
GLY
230
12
1_555
H
HOH
525
E
HOH
12
1_555
94
P 42 21 2