0.013870
0.000000
0.002696
0.000000
0.013774
0.000000
0.000000
0.000000
0.013804
0.00000
0.00000
0.00000
CIS PROLINE - PRO H 37
Tulinsky, A.
Mathews, I.I.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
101.00
90.00
72.100
72.600
73.800
C25 H39 N6 O3 S 1
503.681
amino{[(4S)-4-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino)-5-(4-ethylpiperidin-1-yl)-5-oxopentyl]amino}methaniminium
DAPA
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
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
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
51
550
559
10.1107/S0907444994013132
15299843
Active-site mimetic inhibition of thrombin.
1995
UK
Protein Eng.
PRENE9
0859
0269-2139
6
471
The Structure of a Designed Peptidomimetic Inhibitor Complex of Alpha-Thrombin
1993
UK
Blood Coagulation Fibrinolysis
BLFIE7
0796
0957-5235
4
305
Active Site and Exosite Binding of Alpha-Thrombin
1993
US
Biochemistry
BICHAW
0033
0006-2960
18
996
Interactions of a Fluorescent Active-Site-Directed Inhibitor of Thrombin: Dansylarginine N-(3-Ethyl-1,5-Pentanediyl)Amide
1979
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
4096.534
thrombin
3.4.21.5
1
nat
polymer
29780.219
thrombin
3.4.21.5
1
nat
polymer
1534.554
Hirudin
1
man
polymer
503.681
amino{[(4S)-4-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino)-5-(4-ethylpiperidin-1-yl)-5-oxopentyl]amino}methaniminium
1
syn
non-polymer
18.015
water
201
nat
water
Coagulation factor II
Coagulation factor II
no
no
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
L
polypeptide(L)
no
no
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISM
LEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL
QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISM
LEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL
QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE
H
polypeptide(L)
no
yes
NGDFEEIPEE(TYS)L
NGDFEEIPEEYL
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
n
Medicinal leech
sample
6421
Hirudo medicinalis
human
Homo
sample
9606
BLOOD
Homo sapiens
BLOOD
human
Homo
sample
9606
BLOOD
Homo sapiens
BLOOD
2.68
54.11
repository
Initial release
Version format compliance
Atomic model
Database references
Derived calculations
Non-polymer description
Structure summary
Version format compliance
Other
1
0
1995-02-27
1
1
2008-03-03
1
2
2011-07-13
1
3
2012-12-12
Y
1994-10-16
REL
0ZI
amino{[(4S)-4-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino)-5-(4-ethylpiperidin-1-yl)-5-oxopentyl]amino}methaniminium
HOH
water
THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN
IDENTIFIER *L* IS USED FOR RESIDUES 1H - 15 AND CHAIN
IDENTIFIER *H* IS USED FOR RESIDUES 16 - 247. CHAIN
IDENTIFIER *I* IS USED FOR HIRUGEN, THE CARBOXYL TERMINUS
OF HIRUDIN, WHICH OCCUPIES THE EXOSITE.
Inhibitor
dansylarginine-N-(3-ethyl-1,5-pentanediyl)amide
Peptide-like
0ZI
371
4
0ZI
0ZI
371
H
HOH
401
5
HOH
HOH
401
L
HOH
420
5
HOH
HOH
420
L
HOH
437
5
HOH
HOH
437
L
HOH
438
5
HOH
HOH
438
L
HOH
440
5
HOH
HOH
440
L
HOH
444
5
HOH
HOH
444
L
HOH
448
5
HOH
HOH
448
L
HOH
459
5
HOH
HOH
459
L
HOH
492
5
HOH
HOH
492
L
HOH
506
5
HOH
HOH
506
L
HOH
507
5
HOH
HOH
507
L
HOH
512
5
HOH
HOH
512
L
HOH
519
5
HOH
HOH
519
L
HOH
522
5
HOH
HOH
522
L
HOH
548
5
HOH
HOH
548
L
HOH
556
5
HOH
HOH
556
L
HOH
565
5
HOH
HOH
565
L
HOH
587
5
HOH
HOH
587
L
HOH
594
5
HOH
HOH
594
L
HOH
402
5
HOH
HOH
402
H
HOH
403
5
HOH
HOH
403
H
HOH
404
5
HOH
HOH
404
H
HOH
405
5
HOH
HOH
405
H
HOH
406
5
HOH
HOH
406
H
HOH
407
5
HOH
HOH
407
H
HOH
408
5
HOH
HOH
408
H
HOH
409
5
HOH
HOH
409
H
HOH
410
5
HOH
HOH
410
H
HOH
411
5
HOH
HOH
411
H
HOH
412
5
HOH
HOH
412
H
HOH
413
5
HOH
HOH
413
H
HOH
414
5
HOH
HOH
414
H
HOH
415
5
HOH
HOH
415
H
HOH
416
5
HOH
HOH
416
H
HOH
417
5
HOH
HOH
417
H
HOH
418
5
HOH
HOH
418
H
HOH
419
5
HOH
HOH
419
H
HOH
421
5
HOH
HOH
421
H
HOH
422
5
HOH
HOH
422
H
HOH
423
5
HOH
HOH
423
H
HOH
424
5
HOH
HOH
424
H
HOH
425
5
HOH
HOH
425
H
HOH
426
5
HOH
HOH
426
H
HOH
427
5
HOH
HOH
427
H
HOH
428
5
HOH
HOH
428
H
HOH
429
5
HOH
HOH
429
H
HOH
430
5
HOH
HOH
430
H
HOH
431
5
HOH
HOH
431
H
HOH
432
5
HOH
HOH
432
H
HOH
433
5
HOH
HOH
433
H
HOH
434
5
HOH
HOH
434
H
HOH
435
5
HOH
HOH
435
H
HOH
436
5
HOH
HOH
436
H
HOH
439
5
HOH
HOH
439
H
HOH
441
5
HOH
HOH
441
H
HOH
442
5
HOH
HOH
442
H
HOH
443
5
HOH
HOH
443
H
HOH
445
5
HOH
HOH
445
H
HOH
446
5
HOH
HOH
446
H
HOH
447
5
HOH
HOH
447
H
HOH
449
5
HOH
HOH
449
H
HOH
450
5
HOH
HOH
450
H
HOH
451
5
HOH
HOH
451
H
HOH
452
5
HOH
HOH
452
H
HOH
453
5
HOH
HOH
453
H
HOH
454
5
HOH
HOH
454
H
HOH
455
5
HOH
HOH
455
H
HOH
456
5
HOH
HOH
456
H
HOH
457
5
HOH
HOH
457
H
HOH
458
5
HOH
HOH
458
H
HOH
460
5
HOH
HOH
460
H
HOH
461
5
HOH
HOH
461
H
HOH
462
5
HOH
HOH
462
H
HOH
463
5
HOH
HOH
463
H
HOH
464
5
HOH
HOH
464
H
HOH
465
5
HOH
HOH
465
H
HOH
466
5
HOH
HOH
466
H
HOH
467
5
HOH
HOH
467
H
HOH
468
5
HOH
HOH
468
H
HOH
469
5
HOH
HOH
469
H
HOH
470
5
HOH
HOH
470
H
HOH
471
5
HOH
HOH
471
H
HOH
472
5
HOH
HOH
472
H
HOH
473
5
HOH
HOH
473
H
HOH
474
5
HOH
HOH
474
H
HOH
475
5
HOH
HOH
475
H
HOH
476
5
HOH
HOH
476
H
HOH
477
5
HOH
HOH
477
H
HOH
478
5
HOH
HOH
478
H
HOH
479
5
HOH
HOH
479
H
HOH
480
5
HOH
HOH
480
H
HOH
481
5
HOH
HOH
481
H
HOH
482
5
HOH
HOH
482
H
HOH
483
5
HOH
HOH
483
H
HOH
484
5
HOH
HOH
484
H
HOH
485
5
HOH
HOH
485
H
HOH
486
5
HOH
HOH
486
H
HOH
488
5
HOH
HOH
488
H
HOH
489
5
HOH
HOH
489
H
HOH
491
5
HOH
HOH
491
H
HOH
493
5
HOH
HOH
493
H
HOH
494
5
HOH
HOH
494
H
HOH
495
5
HOH
HOH
495
H
HOH
496
5
HOH
HOH
496
H
HOH
497
5
HOH
HOH
497
H
HOH
498
5
HOH
HOH
498
H
HOH
499
5
HOH
HOH
499
H
HOH
500
5
HOH
HOH
500
H
HOH
501
5
HOH
HOH
501
H
HOH
502
5
HOH
HOH
502
H
HOH
503
5
HOH
HOH
503
H
HOH
504
5
HOH
HOH
504
H
HOH
505
5
HOH
HOH
505
H
HOH
508
5
HOH
HOH
508
H
HOH
509
5
HOH
HOH
509
H
HOH
510
5
HOH
HOH
510
H
HOH
511
5
HOH
HOH
511
H
HOH
513
5
HOH
HOH
513
H
HOH
514
5
HOH
HOH
514
H
HOH
515
5
HOH
HOH
515
H
HOH
516
5
HOH
HOH
516
H
HOH
517
5
HOH
HOH
517
H
HOH
518
5
HOH
HOH
518
H
HOH
520
5
HOH
HOH
520
H
HOH
521
5
HOH
HOH
521
H
HOH
523
5
HOH
HOH
523
H
HOH
524
5
HOH
HOH
524
H
HOH
525
5
HOH
HOH
525
H
HOH
527
5
HOH
HOH
527
H
HOH
528
5
HOH
HOH
528
H
HOH
529
5
HOH
HOH
529
H
HOH
530
5
HOH
HOH
530
H
HOH
531
5
HOH
HOH
531
H
HOH
532
5
HOH
HOH
532
H
HOH
533
5
HOH
HOH
533
H
HOH
534
5
HOH
HOH
534
H
HOH
535
5
HOH
HOH
535
H
HOH
536
5
HOH
HOH
536
H
HOH
537
5
HOH
HOH
537
H
HOH
538
5
HOH
HOH
538
H
HOH
540
5
HOH
HOH
540
H
HOH
541
5
HOH
HOH
541
H
HOH
542
5
HOH
HOH
542
H
HOH
543
5
HOH
HOH
543
H
HOH
544
5
HOH
HOH
544
H
HOH
545
5
HOH
HOH
545
H
HOH
546
5
HOH
HOH
546
H
HOH
547
5
HOH
HOH
547
H
HOH
549
5
HOH
HOH
549
H
HOH
550
5
HOH
HOH
550
H
HOH
551
5
HOH
HOH
551
H
HOH
552
5
HOH
HOH
552
H
HOH
553
5
HOH
HOH
553
H
HOH
554
5
HOH
HOH
554
H
HOH
555
5
HOH
HOH
555
H
HOH
557
5
HOH
HOH
557
H
HOH
558
5
HOH
HOH
558
H
HOH
559
5
HOH
HOH
559
H
HOH
560
5
HOH
HOH
560
H
HOH
561
5
HOH
HOH
561
H
HOH
562
5
HOH
HOH
562
H
HOH
563
5
HOH
HOH
563
H
HOH
564
5
HOH
HOH
564
H
HOH
566
5
HOH
HOH
566
H
HOH
567
5
HOH
HOH
567
H
HOH
568
5
HOH
HOH
568
H
HOH
569
5
HOH
HOH
569
H
HOH
570
5
HOH
HOH
570
H
HOH
571
5
HOH
HOH
571
H
HOH
572
5
HOH
HOH
572
H
HOH
573
5
HOH
HOH
573
H
HOH
574
5
HOH
HOH
574
H
HOH
575
5
HOH
HOH
575
H
HOH
576
5
HOH
HOH
576
H
HOH
577
5
HOH
HOH
577
H
HOH
578
5
HOH
HOH
578
H
HOH
579
5
HOH
HOH
579
H
HOH
580
5
HOH
HOH
580
H
HOH
581
5
HOH
HOH
581
H
HOH
582
5
HOH
HOH
582
H
HOH
583
5
HOH
HOH
583
H
HOH
584
5
HOH
HOH
584
H
HOH
585
5
HOH
HOH
585
H
HOH
586
5
HOH
HOH
586
H
HOH
588
5
HOH
HOH
588
H
HOH
589
5
HOH
HOH
589
H
HOH
590
5
HOH
HOH
590
H
HOH
592
5
HOH
HOH
592
H
HOH
593
5
HOH
HOH
593
H
HOH
595
5
HOH
HOH
595
H
HOH
596
5
HOH
HOH
596
H
HOH
597
5
HOH
HOH
597
H
HOH
598
5
HOH
HOH
598
H
HOH
599
5
HOH
HOH
599
H
HOH
600
5
HOH
HOH
600
H
HOH
601
5
HOH
HOH
601
H
HOH
602
5
HOH
HOH
602
H
HOH
603
5
HOH
HOH
603
H
HOH
604
5
HOH
HOH
604
H
HOH
487
5
HOH
HOH
487
I
HOH
526
5
HOH
HOH
526
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
n
7
B
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
ASN
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
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
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
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
GLY
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
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
n
257
245
H
n
258
246
H
n
259
247
H
n
1
53
I
n
2
54
I
ASP
55
n
3
ASP
55
I
PHE
56
n
4
PHE
56
I
GLU
57
n
5
GLU
57
I
GLU
58
n
6
GLU
58
I
ILE
59
n
7
ILE
59
I
PRO
60
n
8
PRO
60
I
GLU
61
n
9
GLU
61
I
GLU
62
n
10
GLU
62
I
TYS
63
n
11
TYS
63
I
LEU
64
n
12
LEU
64
I
author_and_software_defined_assembly
PISA
3
trimeric
4940
-4
12040
I
TYS
63
O-SULFO-L-TYROSINE
C
TYS
11
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
1
H
HOH
409
F
HOH
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
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
1
H
CG
LYS
145
B
CG
LYS
145
1
Y
1
H
CD
LYS
145
B
CD
LYS
145
1
Y
1
H
CE
LYS
145
B
CE
LYS
145
1
Y
1
H
NZ
LYS
145
B
NZ
LYS
145
1
Y
1
H
CD
LYS
240
B
CD
LYS
252
1
Y
1
H
CE
LYS
240
B
CE
LYS
252
1
Y
1
H
NZ
LYS
240
B
NZ
LYS
252
1
Y
1
H
CG
ASP
243
B
CG
ASP
255
1
Y
1
H
OD1
ASP
243
B
OD1
ASP
255
1
Y
1
H
OD2
ASP
243
B
OD2
ASP
255
1
Y
1
I
CB
GLU
61
C
CB
GLU
9
1
Y
1
I
CG
GLU
61
C
CG
GLU
9
1
Y
1
I
CD
GLU
61
C
CD
GLU
9
1
Y
1
I
OE1
GLU
61
C
OE1
GLU
9
1
Y
1
I
OE2
GLU
61
C
OE2
GLU
9
1
Y
1
I
CG
GLU
62
C
CG
GLU
10
1
Y
1
I
CD
GLU
62
C
CD
GLU
10
1
Y
1
I
OE1
GLU
62
C
OE1
GLU
10
1
Y
1
I
OE2
GLU
62
C
OE2
GLU
10
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
B
1
L
ALA
1
A
ALA
7
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
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
1
H
PHE
245
B
PHE
257
1
Y
1
H
GLY
246
B
GLY
258
1
Y
1
H
GLU
247
B
GLU
259
1
Y
1
I
ASN
53
C
ASN
1
1
Y
1
I
GLY
54
C
GLY
2
1
Y
1
H
H
NH1
OE1
ARG
GLU
50
86
2.13
1
H
ARG
233
10.14
1
H
TYR
94
0.074
SIDE CHAIN
1
H
ARG
165
0.119
SIDE CHAIN
1
8.53
1.40
123.60
132.13
L
L
L
CD
NE
CZ
ARG
ARG
ARG
4
4
4
N
1
5.68
0.90
118.30
123.98
H
H
H
CB
CG
OD1
ASP
ASP
ASP
21
21
21
N
1
-8.67
1.40
110.10
101.43
H
H
H
N
CA
CB
ALA
ALA
ALA
22
22
22
N
1
7.14
1.10
119.40
126.54
H
H
H
NH1
CZ
NH2
ARG
ARG
ARG
35
35
35
N
1
-7.55
0.50
120.30
112.75
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
35
35
35
N
1
8.93
1.10
114.20
123.13
H
H
H
CA
CB
SG
CYS
CYS
CYS
42
42
42
N
1
7.32
0.90
118.30
125.62
H
H
H
CB
CG
OD2
ASP
ASP
ASP
49
49
49
N
1
5.98
0.50
120.30
126.28
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
50
50
50
N
A
A
A
1
5.24
0.60
121.00
126.24
H
H
H
CB
CG
CD2
TYR
TYR
TYR
60
60
60
N
A
A
A
1
-7.66
0.60
121.00
113.34
H
H
H
CB
CG
CD1
TYR
TYR
TYR
60
60
60
N
1
5.53
0.50
120.30
125.83
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
67
67
67
N
1
3.41
0.50
120.30
123.71
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
73
73
73
N
1
-12.59
1.90
110.30
97.71
H
H
H
N
CA
CB
THR
THR
THR
74
74
74
N
A
A
A
1
12.45
1.80
110.60
123.05
H
H
H
N
CA
CB
ARG
ARG
ARG
77
77
77
N
A
A
A
1
-4.25
0.50
120.30
116.05
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
77
77
77
N
A
A
A
1
-19.02
2.10
120.10
101.08
H
H
H
CA
C
O
ARG
ARG
ARG
77
77
77
N
A
A
1
20.83
2.20
117.20
138.03
H
H
H
CA
C
N
ARG
ARG
ASN
77
77
78
Y
1
-4.68
0.60
121.00
116.32
H
H
H
CB
CG
CD2
TYR
TYR
TYR
94
94
94
N
1
-9.19
1.40
123.60
114.41
H
H
H
CD
NE
CZ
ARG
ARG
ARG
97
97
97
N
1
-3.30
0.50
120.30
117.00
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
97
97
97
N
1
5.92
0.50
120.30
126.22
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
101
101
101
N
1
-6.74
0.50
120.30
113.56
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
101
101
101
N
1
-8.23
0.90
118.30
110.07
H
H
H
CB
CG
OD2
ASP
ASP
ASP
102
102
102
N
1
6.53
0.90
118.30
124.83
H
H
H
CB
CG
OD1
ASP
ASP
ASP
116
116
116
N
1
-7.79
0.90
118.30
110.51
H
H
H
CB
CG
OD1
ASP
ASP
ASP
125
125
125
N
1
6.90
0.90
118.30
125.20
H
H
H
CB
CG
OD2
ASP
ASP
ASP
125
125
125
N
1
4.32
0.50
120.30
124.62
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
126
126
126
N
A
A
A
1
10.19
1.40
110.10
120.29
H
H
H
N
CA
CB
ALA
ALA
ALA
129
129
129
N
1
4.13
0.50
120.30
124.43
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
165
165
165
N
1
-5.52
0.50
120.30
114.78
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
165
165
165
N
1
9.04
1.40
123.60
132.64
H
H
H
CD
NE
CZ
ARG
ARG
ARG
173
173
173
N
1
5.99
0.50
120.30
126.29
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
173
173
173
N
1
-5.24
0.50
120.30
115.06
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
175
175
175
N
1
12.69
2.00
110.90
123.59
H
H
H
CA
CB
CG2
ILE
ILE
ILE
176
176
176
N
A
A
A
1
-3.75
0.60
121.00
117.25
H
H
H
CB
CG
CD2
TYR
TYR
TYR
184
184
184
N
1
6.21
0.50
120.30
126.51
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
187
187
187
N
1
-6.82
0.50
120.30
113.48
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
187
187
187
N
1
14.99
2.20
113.40
128.39
H
H
H
CA
CB
CG
GLU
GLU
GLU
192
192
192
N
1
56.26
1.40
123.60
179.86
H
H
H
CD
NE
CZ
ARG
ARG
ARG
206
206
206
N
1
-4.67
0.60
121.00
116.33
H
H
H
CB
CG
CD1
TYR
TYR
TYR
208
208
208
N
A
A
A
1
-11.11
1.40
123.60
112.49
H
H
H
CD
NE
CZ
ARG
ARG
ARG
221
221
221
N
A
A
A
1
6.92
1.10
119.40
126.32
H
H
H
NH1
CZ
NH2
ARG
ARG
ARG
221
221
221
N
A
A
A
1
-10.16
0.50
120.30
110.14
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
221
221
221
N
A
A
A
1
3.21
0.50
120.30
123.51
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
221
221
221
N
1
3.91
0.50
120.30
124.21
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
233
233
233
N
1
-6.33
0.50
120.30
113.97
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
233
233
233
N
1
L
PHE
7
-138.83
-76.28
A
1
H
SER
36
-166.65
107.49
A
1
H
TYR
60
-153.28
78.83
G
1
H
ASN
60
-169.75
79.67
1
H
HIS
71
-130.79
-50.42
A
1
H
GLU
97
-131.77
-51.82
1
H
SER
115
-173.29
-177.69
1
H
SER
195
-31.19
136.74
1
H
SER
214
-85.93
-96.29
0.147
2.3
1
2.3
201
2527
35
0
2291
0.20
5.7
refinement
PROLSQ
ALPHA-THROMBIN (E.C.3.4.21.5) TERNARY COMPLEX WITH EXOSITE INHIBITOR HIRUGEN AND ACTIVE SITE INHIBITOR DANSYLARGININE N-(3-ETHYL-1,5-PENTANEDIYL)AMIDE (DAPA)
ACTIVE SITE MIMETIC INHIBITION OF THROMBIN
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
5
N
N
5
N
N
H
ALA
55
B
ALA
41
HELX_P
H
LEU
60
B
LEU
46
1
H1
6
H
GLU
164
B
GLU
169
HELX_P
H
SER
171
B
SER
176
1
H2
8
H
ASP
125
B
ASP
122
HELX_P
H
LEU
129
B
LEU
129
1
H3
8
C
H
VAL
231
B
VAL
243
HELX_P
H
GLN
244
B
GLN
256
1
H4
14
disulf
2.040
L
CYS
1
A
SG
CYS
9
1_555
H
CYS
122
B
SG
CYS
119
1_555
disulf
2.036
H
CYS
42
B
SG
CYS
28
1_555
H
CYS
58
B
SG
CYS
44
1_555
disulf
2.039
H
CYS
168
B
SG
CYS
173
1_555
H
CYS
182
B
SG
CYS
187
1_555
disulf
2.136
H
CYS
191
B
SG
CYS
201
1_555
H
CYS
220
B
SG
CYS
231
1_555
HYDROLASE/HYDROLASE INHIBITOR
SERINE PROTEASE-INHIBITOR complex, HYDROLASE-HYDROLASE INHIBITOR complex
H
SER
36
B
SER
22
A
1
H
PRO
37
B
PRO
23
-1.61
THRB_HUMAN
UNP
1
328
P00734
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
THRB_HUMAN
UNP
2
364
P00734
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISM
LEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL
QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE
HIR2_HIRME
UNP
3
53
P28504
DGDFEEIPEEYL
328
363
1FPC
1
14
P00734
H
N
L
1
1
36
364
622
1FPC
16
247
P00734
H
2
1
259
53
64
1FPC
53
64
P28504
I
3
1
12
3
ASP
CONFLICT
ASN
53
1FPC
I
P28504
UNP
53
1
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
PRO
28
B
PRO
13
H
ARG
35
B
ARG
20
H
CYS
42
B
CYS
28
H
ASP
49
B
ASP
35
H
ARG
50
B
ARG
36
H
ALA
56
B
ALA
42
H
ARG
101
B
ARG
98
H
LYS
110
B
LYS
107
H
LYS
81
B
LYS
77
H
PRO
92
B
PRO
88
H
ASP
63
B
ASP
58
H
GLY
69
B
GLY
64
H
PRO
28
B
PRO
13
H
ARG
35
B
ARG
20
H
GLY
133
B
GLY
133
H
TRP
141
B
TRP
141
H
LEU
155
B
LEU
160
H
ILE
162
B
ILE
167
H
ASN
179
B
ASN
184
H
PRO
186
B
PRO
192
H
GLY
223
B
GLY
235
H
THR
229
B
THR
241
H
ILE
212
B
ILE
224
H
GLU
217
B
GLU
229
H
GLY
193
B
GLY
203
H
MET
201
B
MET
211
H
GLY
133
B
GLY
133
H
TRP
141
B
TRP
141
BINDING SITE FOR RESIDUE 0ZI H 371
Software
16
BINDING SITE FOR CHAIN I OF HIRUDIN
Software
17
H
HIS
57
B
HIS
43
16
1_555
H
TYR
60
B
TYR
47
A
16
1_555
H
LYS
60
B
LYS
52
F
16
1_555
H
GLU
97
B
GLU
94
A
16
1_555
H
LEU
99
B
LEU
96
16
1_555
H
ASP
189
B
ASP
199
16
1_555
H
ALA
190
B
ALA
200
16
1_555
H
CYS
191
B
CYS
201
16
1_555
H
GLU
192
B
GLU
202
16
1_555
H
TRP
215
B
TRP
227
16
1_555
H
GLY
216
B
GLY
228
16
1_555
H
GLY
219
B
GLY
230
16
1_555
H
CYS
220
B
CYS
231
16
1_555
H
HOH
454
F
HOH
16
1_555
H
HOH
476
F
HOH
16
1_555
H
HOH
564
F
HOH
16
1_555
H
PHE
34
B
PHE
19
17
1_555
H
LYS
36
B
LYS
21
17
1_555
H
GLN
38
B
GLN
24
17
1_555
H
ARG
73
B
ARG
68
17
1_555
H
THR
74
B
THR
69
17
1_555
H
ARG
75
B
ARG
70
17
1_555
H
ARG
75
B
ARG
70
17
2_555
H
TYR
76
B
TYR
71
17
1_555
H
GLU
80
B
GLU
76
17
1_555
H
LYS
81
B
LYS
77
17
1_555
H
ILE
82
B
ILE
78
17
1_555
H
MET
84
B
MET
80
17
1_555
H
SER
153
B
SER
158
17
2_555
H
HOH
462
F
HOH
17
1_555
H
HOH
488
F
HOH
17
2_555
I
HOH
487
G
HOH
17
1_555
I
HOH
526
G
HOH
17
1_555
5
C 1 2 1