0.013974
0.000000
0.002767
0.000000
0.013877
0.000000
0.000000
0.000000
0.013923
0.00000
0.00000
0.00000
Chirgadze, N.Y.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
101.20
90.00
71.560
72.060
73.220
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
C22 H24 N4 O
360.452
2-(4-benzylpiperidine-1-carbonyl)-1H-indole-5-carboximidamide
5-amidinoindole-4-benzylpiperidin
non-polymer
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
C8 H15 N O6
221.208
2-acetamido-2-deoxy-beta-D-glucopyranose
N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE
D-saccharide, beta 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
US
Protein Sci.
PRCIEI
0795
0961-8368
6
1412
1417
9232642
The crystal structure of human alpha-thrombin complexed with LY178550, a nonpeptidyl, active site-directed inhibitor.
1997
BPP B 400 HAS WRONG CHIRALITY AT ATOM C3
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
295
1
YALE/MSC MIRRORS
IMAGE PLATE
1997-01-01
RIGAKU RAXIS IIC
SINGLE WAVELENGTH
M
x-ray
1
1.54
1.0
1.54
ROTATING ANODE
RIGAKU RU200
4096.534
ALPHA-THROMBIN
3.4.21.5
LIGHT CHAIN
1
man
polymer
29780.219
ALPHA-THROMBIN
3.4.21.5
HEAVY CHAIN
1
man
polymer
1548.580
HIRUGEN
1
nat
polymer
221.208
2-acetamido-2-deoxy-beta-D-glucopyranose
1
man
non-polymer
22.990
SODIUM ION
2
syn
non-polymer
360.452
2-(4-benzylpiperidine-1-carbonyl)-1H-indole-5-carboximidamide
1
syn
non-polymer
18.015
water
116
nat
water
no
no
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
A
polypeptide(L)
no
no
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISM
LEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL
QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISM
LEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL
QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE
B
polypeptide(L)
no
yes
GDFEEIPEE(TYS)LQ
GDFEEIPEEYLQ
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
human
Homo
BLOOD
sample
9606
Homo sapiens
human
Homo
BLOOD
sample
9606
Homo sapiens
medicinal leech
Hirudo
sample
6421
Hirudo medicinalis
1
2.78
55.8
VAPOR DIFFUSION
5.6
30% PEG 4000, 150 mM sodium citrate, 200 mM ammonium acetate, pH 5.6, VAPOR DIFFUSION, temperature 277K
277
chem_comp
database_PDB_caveat
entity
pdbx_chem_comp_identifier
pdbx_entity_nonpoly
pdbx_struct_conn_angle
pdbx_unobs_or_zero_occ_atoms
struct_conn
struct_site
struct_site_gen
chem_comp
entity
pdbx_entity_nonpoly
pdbx_validate_chiral
repository
Initial release
Carbohydrate remediation
repository
Remediation
Version format compliance
Atomic model
Database references
Derived calculations
Non-polymer description
Structure summary
Version format compliance
Advisory
Data collection
Derived calculations
Structure summary
Data collection
Derived calculations
Non-polymer description
Structure summary
1
0
1999-10-20
1
1
2008-04-27
1
2
2011-07-13
1
3
2020-07-29
2
0
2021-04-28
_chem_comp.name
_chem_comp.type
_entity.pdbx_description
_pdbx_entity_nonpoly.name
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr1_symmetry
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.ptnr3_symmetry
_pdbx_struct_conn_angle.value
_struct_conn.conn_type_id
_struct_conn.id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.pdbx_role
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_symmetry
_chem_comp.formula
_chem_comp.formula_weight
_chem_comp.name
_chem_comp.pdbx_synonyms
_entity.formula_weight
_entity.pdbx_description
_pdbx_entity_nonpoly.name
DGlcpNAcb
N-acetyl-b-D-glucopyranosamine
b-D-GlcpNAc
GlcNAc
CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN IN COMPLEX WITH BENZO[B]THIOPHENE
INHIBITOR 4
CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH BENZO[B]THIOPHENE
INHIBITOR 2
CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH BENZO[B]THIOPHENE
INHIBITOR 1
CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH BENZO[B]THIOPHENE
INHIBITOR 3
RCSB
Y
RCSB
1999-10-04
REL
NAG
2-acetamido-2-deoxy-beta-D-glucopyranose
NA
SODIUM ION
BPP
2-(4-benzylpiperidine-1-carbonyl)-1H-indole-5-carboximidamide
HOH
water
NAG
500
4
NAG
NAG
500
B
NA
398
5
NA
NA
398
B
NA
399
5
NA
NA
399
B
BPP
400
6
BPP
BPP
400
B
HOH
526
7
HOH
HOH
526
A
HOH
531
7
HOH
HOH
531
A
HOH
552
7
HOH
HOH
552
A
HOH
557
7
HOH
HOH
557
A
HOH
558
7
HOH
HOH
558
A
HOH
560
7
HOH
HOH
560
A
HOH
586
7
HOH
HOH
586
A
HOH
589
7
HOH
HOH
589
A
HOH
592
7
HOH
HOH
592
A
HOH
594
7
HOH
HOH
594
A
HOH
610
7
HOH
HOH
610
A
HOH
621
7
HOH
HOH
621
A
HOH
624
7
HOH
HOH
624
A
HOH
625
7
HOH
HOH
625
A
HOH
501
7
HOH
HOH
501
B
HOH
502
7
HOH
HOH
502
B
HOH
503
7
HOH
HOH
503
B
HOH
504
7
HOH
HOH
504
B
HOH
505
7
HOH
HOH
505
B
HOH
506
7
HOH
HOH
506
B
HOH
507
7
HOH
HOH
507
B
HOH
508
7
HOH
HOH
508
B
HOH
509
7
HOH
HOH
509
B
HOH
510
7
HOH
HOH
510
B
HOH
511
7
HOH
HOH
511
B
HOH
512
7
HOH
HOH
512
B
HOH
513
7
HOH
HOH
513
B
HOH
514
7
HOH
HOH
514
B
HOH
515
7
HOH
HOH
515
B
HOH
516
7
HOH
HOH
516
B
HOH
517
7
HOH
HOH
517
B
HOH
518
7
HOH
HOH
518
B
HOH
519
7
HOH
HOH
519
B
HOH
520
7
HOH
HOH
520
B
HOH
521
7
HOH
HOH
521
B
HOH
522
7
HOH
HOH
522
B
HOH
523
7
HOH
HOH
523
B
HOH
524
7
HOH
HOH
524
B
HOH
525
7
HOH
HOH
525
B
HOH
527
7
HOH
HOH
527
B
HOH
528
7
HOH
HOH
528
B
HOH
529
7
HOH
HOH
529
B
HOH
530
7
HOH
HOH
530
B
HOH
532
7
HOH
HOH
532
B
HOH
533
7
HOH
HOH
533
B
HOH
534
7
HOH
HOH
534
B
HOH
535
7
HOH
HOH
535
B
HOH
536
7
HOH
HOH
536
B
HOH
537
7
HOH
HOH
537
B
HOH
538
7
HOH
HOH
538
B
HOH
539
7
HOH
HOH
539
B
HOH
540
7
HOH
HOH
540
B
HOH
541
7
HOH
HOH
541
B
HOH
542
7
HOH
HOH
542
B
HOH
543
7
HOH
HOH
543
B
HOH
544
7
HOH
HOH
544
B
HOH
545
7
HOH
HOH
545
B
HOH
546
7
HOH
HOH
546
B
HOH
547
7
HOH
HOH
547
B
HOH
548
7
HOH
HOH
548
B
HOH
549
7
HOH
HOH
549
B
HOH
550
7
HOH
HOH
550
B
HOH
551
7
HOH
HOH
551
B
HOH
553
7
HOH
HOH
553
B
HOH
554
7
HOH
HOH
554
B
HOH
555
7
HOH
HOH
555
B
HOH
556
7
HOH
HOH
556
B
HOH
559
7
HOH
HOH
559
B
HOH
561
7
HOH
HOH
561
B
HOH
562
7
HOH
HOH
562
B
HOH
563
7
HOH
HOH
563
B
HOH
564
7
HOH
HOH
564
B
HOH
565
7
HOH
HOH
565
B
HOH
566
7
HOH
HOH
566
B
HOH
567
7
HOH
HOH
567
B
HOH
568
7
HOH
HOH
568
B
HOH
569
7
HOH
HOH
569
B
HOH
570
7
HOH
HOH
570
B
HOH
571
7
HOH
HOH
571
B
HOH
572
7
HOH
HOH
572
B
HOH
573
7
HOH
HOH
573
B
HOH
575
7
HOH
HOH
575
B
HOH
576
7
HOH
HOH
576
B
HOH
577
7
HOH
HOH
577
B
HOH
578
7
HOH
HOH
578
B
HOH
579
7
HOH
HOH
579
B
HOH
581
7
HOH
HOH
581
B
HOH
582
7
HOH
HOH
582
B
HOH
583
7
HOH
HOH
583
B
HOH
584
7
HOH
HOH
584
B
HOH
588
7
HOH
HOH
588
B
HOH
590
7
HOH
HOH
590
B
HOH
591
7
HOH
HOH
591
B
HOH
593
7
HOH
HOH
593
B
HOH
595
7
HOH
HOH
595
B
HOH
596
7
HOH
HOH
596
B
HOH
599
7
HOH
HOH
599
B
HOH
600
7
HOH
HOH
600
B
HOH
601
7
HOH
HOH
601
B
HOH
603
7
HOH
HOH
603
B
HOH
604
7
HOH
HOH
604
B
HOH
605
7
HOH
HOH
605
B
HOH
609
7
HOH
HOH
609
B
HOH
612
7
HOH
HOH
612
B
HOH
613
7
HOH
HOH
613
B
HOH
614
7
HOH
HOH
614
B
HOH
615
7
HOH
HOH
615
B
HOH
616
7
HOH
HOH
616
B
HOH
617
7
HOH
HOH
617
B
HOH
618
7
HOH
HOH
618
B
HOH
619
7
HOH
HOH
619
B
HOH
620
7
HOH
HOH
620
B
HOH
622
7
HOH
HOH
622
B
HOH
623
7
HOH
HOH
623
B
HOH
626
7
HOH
HOH
626
B
HOH
627
7
HOH
HOH
627
B
n
1
1
A
n
2
2
A
n
3
3
A
n
4
4
A
n
5
5
A
GLU
6
n
6
GLU
6
A
ALA
7
n
7
ALA
7
A
ASP
8
n
8
ASP
8
A
CYS
9
n
9
CYS
9
A
GLY
10
n
10
GLY
10
A
LEU
11
n
11
LEU
11
A
ARG
12
n
12
ARG
12
A
PRO
13
n
13
PRO
13
A
LEU
14
n
14
LEU
14
A
PHE
15
n
15
PHE
15
A
GLU
16
n
16
GLU
16
A
LYS
17
n
17
LYS
17
A
LYS
18
n
18
LYS
18
A
SER
19
n
19
SER
19
A
LEU
20
n
20
LEU
20
A
GLU
21
n
21
GLU
21
A
ASP
22
n
22
ASP
22
A
LYS
23
n
23
LYS
23
A
THR
24
n
24
THR
24
A
GLU
25
n
25
GLU
25
A
ARG
26
n
26
ARG
26
A
GLU
27
n
27
GLU
27
A
LEU
28
n
28
LEU
28
A
LEU
29
n
29
LEU
29
A
GLU
30
n
30
GLU
30
A
SER
31
n
31
SER
31
A
TYR
32
n
32
TYR
32
A
ILE
33
n
33
ILE
33
A
n
34
34
A
n
35
35
A
n
36
36
A
ILE
37
n
1
ILE
37
B
VAL
38
n
2
VAL
38
B
GLU
39
n
3
GLU
39
B
GLY
40
n
4
GLY
40
B
SER
41
n
5
SER
41
B
ASP
42
n
6
ASP
42
B
ALA
43
n
7
ALA
43
B
GLU
44
n
8
GLU
44
B
ILE
45
n
9
ILE
45
B
GLY
46
n
10
GLY
46
B
MET
47
n
11
MET
47
B
SER
48
n
12
SER
48
B
PRO
49
n
13
PRO
49
B
TRP
50
n
14
TRP
50
B
GLN
51
n
15
GLN
51
B
VAL
52
n
16
VAL
52
B
MET
53
n
17
MET
53
B
LEU
54
n
18
LEU
54
B
PHE
55
n
19
PHE
55
B
ARG
56
n
20
ARG
56
B
LYS
57
n
21
LYS
57
B
SER
58
n
22
SER
58
B
PRO
59
n
23
PRO
59
B
GLN
60
n
24
GLN
60
B
GLU
61
n
25
GLU
61
B
LEU
62
n
26
LEU
62
B
LEU
63
n
27
LEU
63
B
CYS
64
n
28
CYS
64
B
GLY
65
n
29
GLY
65
B
ALA
66
n
30
ALA
66
B
SER
67
n
31
SER
67
B
LEU
68
n
32
LEU
68
B
ILE
69
n
33
ILE
69
B
SER
70
n
34
SER
70
B
ASP
71
n
35
ASP
71
B
ARG
72
n
36
ARG
72
B
TRP
73
n
37
TRP
73
B
VAL
74
n
38
VAL
74
B
LEU
75
n
39
LEU
75
B
THR
76
n
40
THR
76
B
ALA
77
n
41
ALA
77
B
ALA
78
n
42
ALA
78
B
HIS
79
n
43
HIS
79
B
CYS
80
n
44
CYS
80
B
LEU
81
n
45
LEU
81
B
LEU
82
n
46
LEU
82
B
TYR
83
n
47
TYR
83
B
PRO
84
n
48
PRO
84
B
PRO
85
n
49
PRO
85
B
TRP
86
n
50
TRP
86
B
ASP
87
n
51
ASP
87
B
LYS
88
n
52
LYS
88
B
ASN
89
n
53
ASN
89
B
PHE
90
n
54
PHE
90
B
THR
91
n
55
THR
91
B
GLU
92
n
56
GLU
92
B
ASN
93
n
57
ASN
93
B
ASP
94
n
58
ASP
94
B
LEU
95
n
59
LEU
95
B
LEU
96
n
60
LEU
96
B
VAL
97
n
61
VAL
97
B
ARG
98
n
62
ARG
98
B
ILE
99
n
63
ILE
99
B
GLY
100
n
64
GLY
100
B
LYS
101
n
65
LYS
101
B
HIS
102
n
66
HIS
102
B
SER
103
n
67
SER
103
B
ARG
104
n
68
ARG
104
B
THR
105
n
69
THR
105
B
ARG
106
n
70
ARG
106
B
TYR
107
n
71
TYR
107
B
GLU
108
n
72
GLU
108
B
ARG
109
n
73
ARG
109
B
ASN
110
n
74
ASN
110
B
ILE
111
n
75
ILE
111
B
GLU
112
n
76
GLU
112
B
LYS
113
n
77
LYS
113
B
ILE
114
n
78
ILE
114
B
SER
115
n
79
SER
115
B
MET
116
n
80
MET
116
B
LEU
117
n
81
LEU
117
B
GLU
118
n
82
GLU
118
B
LYS
119
n
83
LYS
119
B
ILE
120
n
84
ILE
120
B
TYR
121
n
85
TYR
121
B
ILE
122
n
86
ILE
122
B
HIS
123
n
87
HIS
123
B
PRO
124
n
88
PRO
124
B
ARG
125
n
89
ARG
125
B
TYR
126
n
90
TYR
126
B
ASN
127
n
91
ASN
127
B
TRP
128
n
92
TRP
128
B
ARG
129
n
93
ARG
129
B
GLU
130
n
94
GLU
130
B
ASN
131
n
95
ASN
131
B
LEU
132
n
96
LEU
132
B
ASP
133
n
97
ASP
133
B
ARG
134
n
98
ARG
134
B
ASP
135
n
99
ASP
135
B
ILE
136
n
100
ILE
136
B
ALA
137
n
101
ALA
137
B
LEU
138
n
102
LEU
138
B
MET
139
n
103
MET
139
B
LYS
140
n
104
LYS
140
B
LEU
141
n
105
LEU
141
B
LYS
142
n
106
LYS
142
B
LYS
143
n
107
LYS
143
B
PRO
144
n
108
PRO
144
B
VAL
145
n
109
VAL
145
B
ALA
146
n
110
ALA
146
B
PHE
147
n
111
PHE
147
B
SER
148
n
112
SER
148
B
ASP
149
n
113
ASP
149
B
TYR
150
n
114
TYR
150
B
ILE
151
n
115
ILE
151
B
HIS
152
n
116
HIS
152
B
PRO
153
n
117
PRO
153
B
VAL
154
n
118
VAL
154
B
CYS
155
n
119
CYS
155
B
LEU
156
n
120
LEU
156
B
PRO
157
n
121
PRO
157
B
ASP
158
n
122
ASP
158
B
ARG
159
n
123
ARG
159
B
GLU
160
n
124
GLU
160
B
THR
161
n
125
THR
161
B
ALA
162
n
126
ALA
162
B
ALA
163
n
127
ALA
163
B
SER
164
n
128
SER
164
B
LEU
165
n
129
LEU
165
B
LEU
166
n
130
LEU
166
B
GLN
167
n
131
GLN
167
B
ALA
168
n
132
ALA
168
B
GLY
169
n
133
GLY
169
B
TYR
170
n
134
TYR
170
B
LYS
171
n
135
LYS
171
B
GLY
172
n
136
GLY
172
B
ARG
173
n
137
ARG
173
B
VAL
174
n
138
VAL
174
B
THR
175
n
139
THR
175
B
GLY
176
n
140
GLY
176
B
TRP
177
n
141
TRP
177
B
GLY
178
n
142
GLY
178
B
ASN
179
n
143
ASN
179
B
LEU
180
n
144
LEU
180
B
LYS
181
n
145
LYS
181
B
GLU
182
n
146
GLU
182
B
THR
183
n
147
THR
183
B
n
148
184
B
n
149
185
B
n
150
186
B
n
151
187
B
n
152
188
B
n
153
189
B
n
154
190
B
GLY
191
n
155
GLY
191
B
GLN
192
n
156
GLN
192
B
PRO
193
n
157
PRO
193
B
SER
194
n
158
SER
194
B
VAL
195
n
159
VAL
195
B
LEU
196
n
160
LEU
196
B
GLN
197
n
161
GLN
197
B
VAL
198
n
162
VAL
198
B
VAL
199
n
163
VAL
199
B
ASN
200
n
164
ASN
200
B
LEU
201
n
165
LEU
201
B
PRO
202
n
166
PRO
202
B
ILE
203
n
167
ILE
203
B
VAL
204
n
168
VAL
204
B
GLU
205
n
169
GLU
205
B
ARG
206
n
170
ARG
206
B
PRO
207
n
171
PRO
207
B
VAL
208
n
172
VAL
208
B
CYS
209
n
173
CYS
209
B
LYS
210
n
174
LYS
210
B
ASP
211
n
175
ASP
211
B
SER
212
n
176
SER
212
B
THR
213
n
177
THR
213
B
ARG
214
n
178
ARG
214
B
ILE
215
n
179
ILE
215
B
ARG
216
n
180
ARG
216
B
ILE
217
n
181
ILE
217
B
THR
218
n
182
THR
218
B
ASP
219
n
183
ASP
219
B
ASN
220
n
184
ASN
220
B
MET
221
n
185
MET
221
B
PHE
222
n
186
PHE
222
B
CYS
223
n
187
CYS
223
B
ALA
224
n
188
ALA
224
B
GLY
225
n
189
GLY
225
B
TYR
226
n
190
TYR
226
B
LYS
227
n
191
LYS
227
B
PRO
228
n
192
PRO
228
B
ASP
229
n
193
ASP
229
B
GLU
230
n
194
GLU
230
B
GLY
231
n
195
GLY
231
B
LYS
232
n
196
LYS
232
B
ARG
233
n
197
ARG
233
B
GLY
234
n
198
GLY
234
B
ASP
235
n
199
ASP
235
B
ALA
236
n
200
ALA
236
B
CYS
237
n
201
CYS
237
B
GLU
238
n
202
GLU
238
B
GLY
239
n
203
GLY
239
B
ASP
240
n
204
ASP
240
B
SER
241
n
205
SER
241
B
GLY
242
n
206
GLY
242
B
GLY
243
n
207
GLY
243
B
PRO
244
n
208
PRO
244
B
PHE
245
n
209
PHE
245
B
VAL
246
n
210
VAL
246
B
MET
247
n
211
MET
247
B
LYS
248
n
212
LYS
248
B
SER
249
n
213
SER
249
B
PRO
250
n
214
PRO
250
B
PHE
251
n
215
PHE
251
B
ASN
252
n
216
ASN
252
B
ASN
253
n
217
ASN
253
B
ARG
254
n
218
ARG
254
B
TRP
255
n
219
TRP
255
B
TYR
256
n
220
TYR
256
B
GLN
257
n
221
GLN
257
B
MET
258
n
222
MET
258
B
GLY
259
n
223
GLY
259
B
ILE
260
n
224
ILE
260
B
VAL
261
n
225
VAL
261
B
SER
262
n
226
SER
262
B
TRP
263
n
227
TRP
263
B
GLY
264
n
228
GLY
264
B
GLU
265
n
229
GLU
265
B
GLY
266
n
230
GLY
266
B
CYS
267
n
231
CYS
267
B
ASP
268
n
232
ASP
268
B
ARG
269
n
233
ARG
269
B
ASP
270
n
234
ASP
270
B
GLY
271
n
235
GLY
271
B
LYS
272
n
236
LYS
272
B
TYR
273
n
237
TYR
273
B
GLY
274
n
238
GLY
274
B
PHE
275
n
239
PHE
275
B
TYR
276
n
240
TYR
276
B
THR
277
n
241
THR
277
B
HIS
278
n
242
HIS
278
B
VAL
279
n
243
VAL
279
B
PHE
280
n
244
PHE
280
B
ARG
281
n
245
ARG
281
B
LEU
282
n
246
LEU
282
B
LYS
283
n
247
LYS
283
B
LYS
284
n
248
LYS
284
B
TRP
285
n
249
TRP
285
B
ILE
286
n
250
ILE
286
B
GLN
287
n
251
GLN
287
B
LYS
288
n
252
LYS
288
B
VAL
289
n
253
VAL
289
B
ILE
290
n
254
ILE
290
B
ASP
291
n
255
ASP
291
B
GLN
292
n
256
GLN
292
B
PHE
293
n
257
PHE
293
B
n
258
294
B
n
259
295
B
GLY
300
n
1
GLY
300
H
ASP
301
n
2
ASP
301
H
PHE
302
n
3
PHE
302
H
GLU
303
n
4
GLU
303
H
GLU
304
n
5
GLU
304
H
ILE
305
n
6
ILE
305
H
PRO
306
n
7
PRO
306
H
GLU
307
n
8
GLU
307
H
GLU
308
n
9
GLU
308
H
TYS
309
n
10
TYS
309
H
LEU
310
n
11
LEU
310
H
GLN
311
n
12
GLN
311
H
author_defined_assembly
3
trimeric
B
LYS
210
B
O
LYS
174
1_555
B
NA
398
E
NA
NA
1_555
B
THR
213
B
O
THR
177
1_555
80.7
B
LYS
210
B
O
LYS
174
1_555
B
NA
398
E
NA
NA
1_555
B
PHE
251
B
O
PHE
215
4_446
96.6
B
THR
213
B
O
THR
177
1_555
B
NA
398
E
NA
NA
1_555
B
PHE
251
B
O
PHE
215
4_446
95.6
B
LYS
210
B
O
LYS
174
1_555
B
NA
398
E
NA
NA
1_555
B
HOH
549
I
O
HOH
1_555
86.4
B
THR
213
B
O
THR
177
1_555
B
NA
398
E
NA
NA
1_555
B
HOH
549
I
O
HOH
1_555
167.0
B
PHE
251
B
O
PHE
215
4_446
B
NA
398
E
NA
NA
1_555
B
HOH
549
I
O
HOH
1_555
84.6
B
LYS
210
B
O
LYS
174
1_555
B
NA
398
E
NA
NA
1_555
B
HOH
553
I
O
HOH
1_555
165.8
B
THR
213
B
O
THR
177
1_555
B
NA
398
E
NA
NA
1_555
B
HOH
553
I
O
HOH
1_555
86.8
B
PHE
251
B
O
PHE
215
4_446
B
NA
398
E
NA
NA
1_555
B
HOH
553
I
O
HOH
1_555
91.2
B
HOH
549
I
O
HOH
1_555
B
NA
398
E
NA
NA
1_555
B
HOH
553
I
O
HOH
1_555
106.2
B
LYS
210
B
O
LYS
174
1_555
B
NA
398
E
NA
NA
1_555
B
HOH
617
I
O
HOH
1_555
78.4
B
THR
213
B
O
THR
177
1_555
B
NA
398
E
NA
NA
1_555
B
HOH
617
I
O
HOH
1_555
76.6
B
PHE
251
B
O
PHE
215
4_446
B
NA
398
E
NA
NA
1_555
B
HOH
617
I
O
HOH
1_555
171.3
B
HOH
549
I
O
HOH
1_555
B
NA
398
E
NA
NA
1_555
B
HOH
617
I
O
HOH
1_555
102.1
B
HOH
553
I
O
HOH
1_555
B
NA
398
E
NA
NA
1_555
B
HOH
617
I
O
HOH
1_555
92.3
B
ARG
269
B
O
ARG
233
1_555
B
NA
399
F
NA
NA
1_555
B
LYS
272
B
O
LYS
236
1_555
92.1
B
ARG
269
B
O
ARG
233
1_555
B
NA
399
F
NA
NA
1_555
B
HOH
513
I
O
HOH
1_555
149.3
B
LYS
272
B
O
LYS
236
1_555
B
NA
399
F
NA
NA
1_555
B
HOH
513
I
O
HOH
1_555
73.1
B
ARG
269
B
O
ARG
233
1_555
B
NA
399
F
NA
NA
1_555
B
HOH
527
I
O
HOH
1_555
101.3
B
LYS
272
B
O
LYS
236
1_555
B
NA
399
F
NA
NA
1_555
B
HOH
527
I
O
HOH
1_555
90.6
B
HOH
513
I
O
HOH
1_555
B
NA
399
F
NA
NA
1_555
B
HOH
527
I
O
HOH
1_555
105.5
B
ARG
269
B
O
ARG
233
1_555
B
NA
399
F
NA
NA
1_555
B
HOH
555
I
O
HOH
1_555
103.2
B
LYS
272
B
O
LYS
236
1_555
B
NA
399
F
NA
NA
1_555
B
HOH
555
I
O
HOH
1_555
154.5
B
HOH
513
I
O
HOH
1_555
B
NA
399
F
NA
NA
1_555
B
HOH
555
I
O
HOH
1_555
83.7
B
HOH
527
I
O
HOH
1_555
B
NA
399
F
NA
NA
1_555
B
HOH
555
I
O
HOH
1_555
106.0
B
ASN
89
GLYCOSYLATION SITE
B
ASN
53
ASN
H
TYS
309
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
B
O
SER
41
B
O
SER
5
B
N
VAL
198
B
N
VAL
162
B
O
LEU
201
B
O
LEU
165
B
N
GLY
172
B
N
GLY
136
B
N
THR
175
B
N
THR
139
B
O
PRO
244
B
O
PRO
208
B
O
MET
247
B
O
MET
211
B
N
TYR
256
B
N
TYR
220
B
O
TRP
263
B
O
TRP
227
B
N
PHE
275
B
N
PHE
239
B
N
TYR
276
B
N
TYR
240
B
O
PHE
222
B
O
PHE
186
B
N
ARG
56
B
N
ARG
20
B
O
GLU
61
B
O
GLU
25
B
O
ALA
66
B
O
ALA
30
B
N
VAL
52
B
N
VAL
16
B
O
PHE
55
B
O
PHE
19
B
N
LEU
96
B
N
LEU
60
B
N
ILE
99
B
N
ILE
63
B
O
LYS
113
B
O
LYS
77
B
N
TYR
121
B
N
TYR
85
B
O
LEU
138
B
O
LEU
102
B
O
MET
139
B
O
MET
103
B
N
VAL
74
B
N
VAL
38
B
N
TYR
83
B
N
TYR
47
B
O
LYS
88
B
O
LYS
52
1
A
THR
1
A
THR
1
1
Y
1
A
PHE
2
A
PHE
2
1
Y
1
A
GLY
3
A
GLY
3
1
Y
1
A
SER
4
A
SER
4
1
Y
1
A
GLY
5
A
GLY
5
1
Y
1
A
ASP
34
A
ASP
34
1
Y
1
A
GLY
35
A
GLY
35
1
Y
1
A
ARG
36
A
ARG
36
1
Y
1
B
TRP
184
B
TRP
148
1
Y
1
B
THR
185
B
THR
149
1
Y
1
B
ALA
186
B
ALA
150
1
Y
1
B
ASN
187
B
ASN
151
1
Y
1
B
VAL
188
B
VAL
152
1
Y
1
B
GLY
189
B
GLY
153
1
Y
1
B
LYS
190
B
LYS
154
1
Y
1
B
GLY
294
B
GLY
258
1
Y
1
B
GLU
295
B
GLU
259
1
Y
1
A
PHE
15
-125.36
-85.35
1
B
SER
70
-171.09
-179.85
1
B
TYR
83
-155.16
84.90
1
B
ASN
89
-158.10
75.70
1
B
HIS
102
-136.53
-51.04
1
B
SER
262
-108.32
-66.64
0.231
0.184
0.184
2.07
20.00
935
19256
4.2
88.4
RANDOM
1
2.000
2.07
20.00
116
2522
43
0
2363
0.009
1.38
26.42
0.78
0.243
0.215
2.16
1903
8
3.2
73.8
2.070
30.000
1D4P
21650
0.000
0.065
1
18.4000
2.700
97.3
0.253
2.07
2.11
3.6
1
2.70
99.4
data reduction
DENZO
data scaling
SCALEPACK
phasing
AMoRE
refinement
X-PLOR
98.0
ALPHA-THROMBIN (E.C.3.4.21.5)
CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH 5-AMIDINOINDOLE-4-BENZYLPIPERIDINE INHIBITOR
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
5
N
N
6
N
N
7
N
N
7
N
N
A
PHE
15
A
PHE
15
HELX_P
A
SER
19
A
SER
19
5
1
5
A
THR
24
A
THR
24
HELX_P
A
TYR
32
A
TYR
32
1
2
9
B
ALA
77
B
ALA
41
HELX_P
B
CYS
80
B
CYS
44
5
3
4
B
PRO
84
B
PRO
48
HELX_P
B
ASP
87
B
ASP
51
5
4
4
B
THR
91
B
THR
55
HELX_P
B
ASN
93
B
ASN
57
5
5
3
B
ASP
158
B
ASP
122
HELX_P
B
LEU
166
B
LEU
130
1
6
9
B
GLU
205
B
GLU
169
HELX_P
B
ASP
211
B
ASP
175
1
7
7
B
LEU
282
B
LEU
246
HELX_P
B
PHE
293
B
PHE
257
1
8
12
disulf
2.020
A
CYS
9
A
SG
CYS
9
1_555
B
CYS
155
B
SG
CYS
119
1_555
disulf
2.031
B
CYS
64
B
SG
CYS
28
1_555
B
CYS
80
B
SG
CYS
44
1_555
disulf
2.027
B
CYS
209
B
SG
CYS
173
1_555
B
CYS
223
B
SG
CYS
187
1_555
disulf
2.031
B
CYS
237
B
SG
CYS
201
1_555
B
CYS
267
B
SG
CYS
231
1_555
covale
1.459
one
N-Glycosylation
B
ASN
89
B
ND2
ASN
53
1_555
B
NAG
500
D
C1
NAG
1_555
covale
1.328
both
H
GLU
308
C
C
GLU
9
1_555
H
TYS
309
C
N
TYS
10
1_555
covale
1.326
both
H
TYS
309
C
C
TYS
10
1_555
H
LEU
310
C
N
LEU
11
1_555
metalc
2.556
B
LYS
210
B
O
LYS
174
1_555
B
NA
398
E
NA
NA
1_555
metalc
2.415
B
THR
213
B
O
THR
177
1_555
B
NA
398
E
NA
NA
1_555
metalc
2.496
B
PHE
251
B
O
PHE
215
4_446
B
NA
398
E
NA
NA
1_555
metalc
2.495
B
ARG
269
B
O
ARG
233
1_555
B
NA
399
F
NA
NA
1_555
metalc
2.403
B
LYS
272
B
O
LYS
236
1_555
B
NA
399
F
NA
NA
1_555
metalc
2.627
B
NA
398
E
NA
NA
1_555
B
HOH
549
I
O
HOH
1_555
metalc
2.397
B
NA
398
E
NA
NA
1_555
B
HOH
553
I
O
HOH
1_555
metalc
2.828
B
NA
398
E
NA
NA
1_555
B
HOH
617
I
O
HOH
1_555
metalc
2.665
B
NA
399
F
NA
NA
1_555
B
HOH
513
I
O
HOH
1_555
metalc
2.390
B
NA
399
F
NA
NA
1_555
B
HOH
527
I
O
HOH
1_555
metalc
2.498
B
NA
399
F
NA
NA
1_555
B
HOH
555
I
O
HOH
1_555
HYDROLASE/HYDROLASE INHIBITOR
THROMBIN; NONPEPTIDYL INHIBITOR; STRUCTURE-BASED DRUG DESIGN, BLOOD CLOTTING, HYDROLASE-HYDROLASE INHIBITOR COMPLEX
B
SER
58
B
SER
22
1
B
PRO
59
B
PRO
23
0.41
THRB_HUMAN
UNP
1
328
P00734
THRB_HUMAN
UNP
2
364
P00734
ITHA_HIRME
UNP
3
54
P28501
328
363
1D4P
1
36
P00734
A
1
1
36
364
622
1D4P
37
295
P00734
B
2
1
259
54
65
1D4P
300
311
P28501
H
3
1
12
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
B
SER
41
B
SER
5
B
ASP
42
B
ASP
6
B
GLN
197
B
GLN
161
B
PRO
202
B
PRO
166
B
LYS
171
B
LYS
135
B
GLY
176
B
GLY
140
B
PRO
244
B
PRO
208
B
LYS
248
B
LYS
212
B
TRP
255
B
TRP
219
B
TRP
263
B
TRP
227
B
GLY
274
B
GLY
238
B
HIS
278
B
HIS
242
B
MET
221
B
MET
185
B
ALA
224
B
ALA
188
B
GLN
51
B
GLN
15
B
ARG
56
B
ARG
20
B
GLU
61
B
GLU
25
B
LEU
68
B
LEU
32
B
GLN
51
B
GLN
15
B
ARG
56
B
ARG
20
B
LEU
95
B
LEU
59
B
ILE
99
B
ILE
63
B
LYS
113
B
LYS
77
B
ILE
122
B
ILE
86
B
ALA
137
B
ALA
101
B
LEU
141
B
LEU
105
B
TRP
73
B
TRP
37
B
THR
76
B
THR
40
B
LEU
82
B
LEU
46
B
TYR
83
B
TYR
47
B
LYS
88
B
LYS
52
B
ASN
89
B
ASN
53
5
C 1 2 1