0.011013
0.000000
0.000000
0.000000
0.011013
0.000000
0.000000
0.000000
0.007547
0.00000
0.00000
0.00000
CIS PROLINE - PRO H 37
Banner, D.W.
Hadvary, P.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
90.800
90.800
132.500
C21 H34 Cl N6 O3 1
453.986
D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide
PPACK
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
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
266
20085
20093
1939071
Crystallographic analysis at 3.0-A resolution of the binding to human thrombin of four active site-directed inhibitors.
1991
IX
Eur.J.Biochem.
EJBCAI
0262
0014-2956
193
175
182
2226434
Geometry of binding of the benzamidine- and arginine-based inhibitors N alpha-(2-naphthyl-sulphonyl-glycyl)-DL-p-amidinophenylalanyl-pipe ridine (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
3475
2583108
The refined 1.9 A crystal structure of human alpha-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segment.
1989
US
Protein Sci.
PRCIEI
0795
0961-8368
1
426
471
1304349
The refined 1.9-A 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
US
Science
SCIEAS
0038
0036-8075
249
277
280
2374926
The structure of a complex of recombinant hirudin and human alpha-thrombin.
1990
IX
Eur.J.Biochem.
EJBCAI
0262
0014-2956
206
187
195
1587268
The interaction of thrombin with fibrinogen. A structural basis for its specificity.
1992
UK
Embo J.
EMJODG
0897
0261-4189
9
2361
2365
2369893
Crystal structure of the thrombin-hirudin complex: a novel mode of serine protease inhibition.
1990
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
ALPHA-THROMBIN light chain
3.4.21.5
1
nat
polymer
29780.219
ALPHA-THROMBIN heavy chain
3.4.21.5
1
nat
polymer
1411.465
HIRUDIN IIIA
1
man
polymer
453.986
D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide
1
syn
non-polymer
18.015
water
55
nat
water
Hirudin IIIA
no
no
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
L
polypeptide(L)
no
no
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISM
LEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL
QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISM
LEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL
QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE
H
polypeptide(L)
no
no
DFEEIPEEYLQ
DFEEIPEEYLQ
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
Medicinal leech
sample
6421
Hirudo medicinalis
human
sample
9606
PLASMA
Homo sapiens
human
sample
9606
PLASMA
Homo sapiens
3.82
67.82
repository
Initial release
Version format compliance
Atomic model
Database references
Derived calculations
Non-polymer description
Structure summary
Version format compliance
Other
1
0
1994-01-31
1
1
2008-03-06
1
2
2011-07-13
1
3
2013-02-27
Y
1992-08-19
REL
0G6
D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide
HOH
water
THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN
INDICATOR *L* IS USED FOR RESIDUES 1H - 15 AND CHAIN
INDICATOR *H* IS USED FOR RESIDUES 16 - 247. CHAIN
INDICATOR *I* IS USED FOR A C-TERMINAL HIRUDIN PEPTIDE
((DES-AMINO ASP55)HIRUDIN(55-65)). THE RESIDUES OF
CHAIN I ARE NUMBERED FROM 1 - 11. IT BINDS IN THE
ANION-BINDING EXOSITE.
PPACK BINDS COVALENTLY TO THE CATALYTIC SERINE (H 195) AND
ALSO TO THE CATALYTIC HISTIDINE (H 57). THE
CHLOROMETHYLKETONE SUBSTITUENT REMAINS ONLY AS A
BRIDGING METHYLENE GROUP CH2 LINKING THE INHIBITOR TO NE2 OF
HIS 57 AND THE ARGININE CARBONYL CARBON BECOMES TETRAHEDRAL
FORMING A HEMIKETAL LINK TO OG OF SER 195.
CHYMOTRYPSIN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS
USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE
STRUCTURE OF CHYMOTRYPSIN (W.BODE ET AL., 1989, EMBO J. 8,
3467-3475).
Inhibitor
D-Phe-Pro-Arg-CH2Cl
Peptide-like
DPN
1
4
0G6
0G6
1
H
HOH
31
5
HOH
HOH
30
L
HOH
53
5
HOH
HOH
48
L
HOH
63
5
HOH
HOH
62
L
HOH
18
5
HOH
HOH
248
H
HOH
20
5
HOH
HOH
249
H
HOH
21
5
HOH
HOH
250
H
HOH
22
5
HOH
HOH
251
H
HOH
23
5
HOH
HOH
252
H
HOH
24
5
HOH
HOH
253
H
HOH
25
5
HOH
HOH
254
H
HOH
26
5
HOH
HOH
255
H
HOH
27
5
HOH
HOH
256
H
HOH
28
5
HOH
HOH
257
H
HOH
30
5
HOH
HOH
258
H
HOH
32
5
HOH
HOH
259
H
HOH
33
5
HOH
HOH
260
H
HOH
34
5
HOH
HOH
261
H
HOH
35
5
HOH
HOH
262
H
HOH
36
5
HOH
HOH
263
H
HOH
37
5
HOH
HOH
264
H
HOH
39
5
HOH
HOH
265
H
HOH
41
5
HOH
HOH
266
H
HOH
42
5
HOH
HOH
267
H
HOH
43
5
HOH
HOH
268
H
HOH
44
5
HOH
HOH
269
H
HOH
46
5
HOH
HOH
270
H
HOH
48
5
HOH
HOH
271
H
HOH
49
5
HOH
HOH
272
H
HOH
50
5
HOH
HOH
273
H
HOH
52
5
HOH
HOH
274
H
HOH
54
5
HOH
HOH
275
H
HOH
55
5
HOH
HOH
276
H
HOH
56
5
HOH
HOH
277
H
HOH
57
5
HOH
HOH
278
H
HOH
60
5
HOH
HOH
279
H
HOH
48
5
HOH
HOH
280
H
HOH
49
5
HOH
HOH
281
H
HOH
50
5
HOH
HOH
282
H
HOH
53
5
HOH
HOH
283
H
HOH
54
5
HOH
HOH
284
H
HOH
55
5
HOH
HOH
285
H
HOH
61
5
HOH
HOH
286
H
HOH
64
5
HOH
HOH
287
H
HOH
65
5
HOH
HOH
288
H
HOH
66
5
HOH
HOH
289
H
HOH
67
5
HOH
HOH
290
H
HOH
68
5
HOH
HOH
291
H
HOH
69
5
HOH
HOH
292
H
HOH
71
5
HOH
HOH
293
H
HOH
47
5
HOH
HOH
294
H
HOH
62
5
HOH
HOH
295
H
HOH
70
5
HOH
HOH
296
H
HOH
16
5
HOH
HOH
16
I
HOH
17
5
HOH
HOH
17
I
HOH
19
5
HOH
HOH
19
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
GLU
1
n
6
C
GLU
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
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
THR
147
n
147
THR
147
H
TRP
148
n
148
TRP
148
H
THR
149
n
149
THR
149
H
ALA
149
n
150
A
ALA
149
H
ASN
149
n
151
B
ASN
149
H
VAL
149
n
152
C
VAL
149
H
GLY
149
n
153
D
GLY
149
H
LYS
149
n
154
E
LYS
149
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
PHE
245
n
257
PHE
245
H
GLY
246
n
258
GLY
246
H
n
259
247
H
ASP
1
n
1
ASP
1
I
PHE
2
n
2
PHE
2
I
GLU
3
n
3
GLU
3
I
GLU
4
n
4
GLU
4
I
ILE
5
n
5
ILE
5
I
PRO
6
n
6
PRO
6
I
GLU
7
n
7
GLU
7
I
GLU
8
n
8
GLU
8
I
TYR
9
n
9
TYR
9
I
LEU
10
n
10
LEU
10
I
GLN
11
n
11
GLN
11
I
author_and_software_defined_assembly
PISA
3
trimeric
4310
-23
13440
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
O
SER
20
B
O
SER
5
H
N
VAL
157
B
N
VAL
162
H
O
LEU
160
B
O
LEU
165
H
N
GLY
136
B
N
GLY
136
H
N
THR
139
B
N
THR
139
H
O
PRO
198
B
O
PRO
208
H
O
MET
201
B
O
MET
211
H
N
TYR
208
B
N
TYR
220
H
O
TRP
215
B
O
TRP
227
H
N
PHE
227
B
N
PHE
239
H
N
TYR
228
B
N
TYR
240
H
O
PHE
181
B
O
PHE
186
H
N
ARG
35
B
N
ARG
20
H
O
GLU
39
B
O
GLU
25
H
N
ILE
47
B
N
ILE
33
H
O
TRP
51
B
O
TRP
37
H
N
THR
54
B
N
THR
40
H
O
ALA
104
B
O
ALA
101
H
O
LYS
107
B
O
LYS
104
H
N
GLU
86
B
N
GLU
82
H
N
LEU
85
B
N
LEU
81
H
O
LEU
64
B
O
LEU
59
H
O
ARG
67
B
O
ARG
62
H
N
MET
32
B
N
MET
17
C
1
L
CG
GLU
1
A
CG
GLU
6
1
Y
C
1
L
CD
GLU
1
A
CD
GLU
6
1
Y
C
1
L
OE1
GLU
1
A
OE1
GLU
6
1
Y
C
1
L
OE2
GLU
1
A
OE2
GLU
6
1
Y
E
1
H
CG
ASP
60
B
CG
ASP
51
1
Y
E
1
H
OD1
ASP
60
B
OD1
ASP
51
1
Y
E
1
H
OD2
ASP
60
B
OD2
ASP
51
1
Y
A
1
H
CG
ARG
77
B
CG
ARG
73
1
Y
A
1
H
CD
ARG
77
B
CD
ARG
73
1
Y
A
1
H
NE
ARG
77
B
NE
ARG
73
1
Y
A
1
H
CZ
ARG
77
B
CZ
ARG
73
1
Y
A
1
H
NH1
ARG
77
B
NH1
ARG
73
1
Y
A
1
H
NH2
ARG
77
B
NH2
ARG
73
1
Y
1
H
CG
LYS
81
B
CG
LYS
77
1
Y
1
H
CD
LYS
81
B
CD
LYS
77
1
Y
1
H
CE
LYS
81
B
CE
LYS
77
1
Y
1
H
NZ
LYS
81
B
NZ
LYS
77
1
Y
1
H
CG
ARG
93
B
CG
ARG
89
1
Y
1
H
CD
ARG
93
B
CD
ARG
89
1
Y
1
H
NE
ARG
93
B
NE
ARG
89
1
Y
1
H
CZ
ARG
93
B
CZ
ARG
89
1
Y
1
H
NH1
ARG
93
B
NH1
ARG
89
1
Y
1
H
NH2
ARG
93
B
NH2
ARG
89
1
Y
1
H
CG
ARG
97
B
CG
ARG
93
1
Y
1
H
CD
ARG
97
B
CD
ARG
93
1
Y
1
H
NE
ARG
97
B
NE
ARG
93
1
Y
1
H
CZ
ARG
97
B
CZ
ARG
93
1
Y
1
H
NH1
ARG
97
B
NH1
ARG
93
1
Y
1
H
NH2
ARG
97
B
NH2
ARG
93
1
Y
1
H
CG
GLU
127
B
CG
GLU
124
1
Y
1
H
CD
GLU
127
B
CD
GLU
124
1
Y
1
H
OE1
GLU
127
B
OE1
GLU
124
1
Y
1
H
OE2
GLU
127
B
OE2
GLU
124
1
Y
E
1
H
CG
LYS
149
B
CG
LYS
154
1
Y
E
1
H
CD
LYS
149
B
CD
LYS
154
1
Y
E
1
H
CE
LYS
149
B
CE
LYS
154
1
Y
E
1
H
NZ
LYS
149
B
NZ
LYS
154
1
Y
1
H
CG
LYS
169
B
CG
LYS
174
1
Y
1
H
CD
LYS
169
B
CD
LYS
174
1
Y
1
H
CE
LYS
169
B
CE
LYS
174
1
Y
1
H
NZ
LYS
169
B
NZ
LYS
174
1
Y
1
H
CG
ARG
173
B
CG
ARG
178
1
Y
1
H
CD
ARG
173
B
CD
ARG
178
1
Y
1
H
NE
ARG
173
B
NE
ARG
178
1
Y
1
H
CZ
ARG
173
B
CZ
ARG
178
1
Y
1
H
NH1
ARG
173
B
NH1
ARG
178
1
Y
1
H
NH2
ARG
173
B
NH2
ARG
178
1
Y
1
H
CA
GLY
246
B
CA
GLY
258
1
Y
1
H
C
GLY
246
B
C
GLY
258
1
Y
1
H
O
GLY
246
B
O
GLY
258
1
Y
1
I
N
ASP
1
C
N
ASP
1
1
Y
1
I
CG
GLU
8
C
CG
GLU
8
1
Y
1
I
CD
GLU
8
C
CD
GLU
8
1
Y
1
I
OE1
GLU
8
C
OE1
GLU
8
1
Y
1
I
OE2
GLU
8
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
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
GLU
247
B
GLU
259
1
Y
1
H
H
OG
O2
SER
0G6
195
1
2.14
1
-5.68
0.90
118.30
112.62
H
H
H
CB
CG
OD1
ASP
ASP
ASP
21
21
21
N
1
5.80
0.90
118.30
124.10
H
H
H
CB
CG
OD2
ASP
ASP
ASP
49
49
49
N
1
-5.69
0.90
118.30
112.61
H
H
H
CB
CG
OD2
ASP
ASP
ASP
63
63
63
N
1
5.47
0.90
118.30
123.77
H
H
H
CB
CG
OD1
ASP
ASP
ASP
100
100
100
N
1
-3.90
0.50
120.30
116.40
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
101
101
101
N
1
-5.72
0.90
118.30
112.58
H
H
H
CB
CG
OD2
ASP
ASP
ASP
102
102
102
N
1
6.02
0.90
118.30
124.32
H
H
H
CB
CG
OD1
ASP
ASP
ASP
116
116
116
N
1
-6.88
0.90
118.30
111.42
H
H
H
CB
CG
OD2
ASP
ASP
ASP
116
116
116
N
1
6.28
0.90
118.30
124.58
H
H
H
CB
CG
OD1
ASP
ASP
ASP
125
125
125
N
1
3.56
0.50
120.30
123.86
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
126
126
126
N
1
6.65
0.90
118.30
124.95
H
H
H
CB
CG
OD1
ASP
ASP
ASP
170
170
170
N
1
-6.96
0.90
118.30
111.34
H
H
H
CB
CG
OD2
ASP
ASP
ASP
170
170
170
N
1
-5.77
0.90
118.30
112.53
H
H
H
CB
CG
OD2
ASP
ASP
ASP
178
178
178
N
A
A
A
1
-6.44
0.90
118.30
111.86
H
H
H
CB
CG
OD1
ASP
ASP
ASP
186
186
186
N
A
A
A
1
6.18
0.90
118.30
124.48
H
H
H
CB
CG
OD2
ASP
ASP
ASP
186
186
186
N
1
3.45
0.50
120.30
123.75
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
187
187
187
N
1
-5.81
0.90
118.30
112.49
H
H
H
CB
CG
OD1
ASP
ASP
ASP
189
189
189
N
1
-6.55
0.90
118.30
111.75
H
H
H
CB
CG
OD1
ASP
ASP
ASP
194
194
194
N
1
5.46
0.90
118.30
123.76
H
H
H
CB
CG
OD2
ASP
ASP
ASP
194
194
194
N
1
-5.45
0.90
118.30
112.85
H
H
H
CB
CG
OD2
ASP
ASP
ASP
243
243
243
N
1
L
L
CD
OE1
GLU
GLU
13
13
0.070
0.011
1.252
1.322
N
E
E
1
L
L
CD
OE1
GLU
GLU
14
14
0.085
0.011
1.252
1.337
N
H
H
1
L
L
CD
OE1
GLU
GLU
14
14
0.067
0.011
1.252
1.319
N
1
H
H
CD
OE2
GLU
GLU
18
18
0.071
0.011
1.252
1.323
N
1
H
H
CD
OE2
GLU
GLU
39
39
0.078
0.011
1.252
1.330
N
1
H
H
CD
OE2
GLU
GLU
77
77
0.081
0.011
1.252
1.333
N
1
H
H
CD
OE2
GLU
GLU
86
86
0.075
0.011
1.252
1.327
N
A
A
1
H
H
CD
OE1
GLU
GLU
97
97
0.103
0.011
1.252
1.355
N
1
H
H
CD
OE2
GLU
GLU
164
164
0.078
0.011
1.252
1.330
N
1
H
H
CD
OE2
GLU
GLU
192
192
0.066
0.011
1.252
1.318
N
1
I
I
CD
OE2
GLU
GLU
4
4
0.079
0.011
1.252
1.331
N
1
I
I
CD
OE2
GLU
GLU
7
7
0.071
0.011
1.252
1.323
N
B
1
L
ALA
1
58.59
128.40
1
L
PHE
7
-131.28
-81.65
1
L
SER
11
57.29
18.93
1
H
SER
27
-155.88
69.39
1
H
PRO
28
-68.49
0.58
1
H
ASP
49
-54.72
-7.01
1
H
ARG
50
-143.92
-3.09
1
H
HIS
57
-53.56
-8.84
A
1
H
TYR
60
-152.26
84.43
G
1
H
ASN
60
-158.51
80.95
1
H
HIS
71
-120.12
-59.71
A
1
H
GLU
97
-140.11
-38.40
B
1
H
ASN
149
67.71
-8.90
C
1
H
VAL
149
-105.93
79.96
1
I
LEU
10
-88.98
30.66
PROLINES ARE TOO FLAT AS A BAD DICTIONARY WAS USED.
ASN H 60G IS GLYCOSYLATED. THE SUGAR ELECTRON DENSITY IS
WEAK AND NO COORDINATES ARE PRESENT FOR THE SUGAR.
0.164
3.0
25.0
1
0.0
3.0
25.0
55
2444
30
0
2359
0.015
1.99
refinement
TNT
ALPHA-THROMBIN (E.C.3.4.21.5) COMPLEX WITH (DES-AMINO ASP 55) HIRUDIN (RESIDUES 55 - 65) AND D-PHE-PRO-ARG-CHLOROMETHYLKETONE (PPACK) WITH CHLOROMETHYLKETONE REPLACED BY A METHYLENE GROUP
Crystallographic analysis at 3.0-Angstroms resolution of the binding to human thrombin of four active site-directed inhibitors
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
5
N
N
5
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
SER
14
A
SER
31
1
2
8
B
I
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
ASP
125
B
ASP
122
HELX_P
H
LEU
130
B
LEU
130
1
5
9
H
GLU
164
B
GLU
169
HELX_P
H
ASP
170
B
ASP
175
1
6
7
H
LYS
185
B
LYS
191
HELX_P
H
GLY
186
B
GLY
195
5
7
5
C
H
VAL
231
B
VAL
243
HELX_P
H
ASP
243
B
ASP
255
1
8
13
disulf
2.002
L
CYS
1
A
SG
CYS
9
1_555
H
CYS
122
B
SG
CYS
119
1_555
disulf
2.038
H
CYS
42
B
SG
CYS
28
1_555
H
CYS
58
B
SG
CYS
44
1_555
disulf
2.048
H
CYS
168
B
SG
CYS
173
1_555
H
CYS
182
B
SG
CYS
187
1_555
disulf
2.035
H
CYS
191
B
SG
CYS
201
1_555
H
CYS
220
B
SG
CYS
231
1_555
covale
1.477
H
SER
195
B
OG
SER
205
1_555
H
0G6
1
D
C2
0G6
1_555
covale
1.506
H
HIS
57
B
NE2
HIS
43
1_555
H
0G6
1
D
C3
0G6
1_555
HYDROLASE/HYDROLASE INHIBITOR
HYDROLASE-HYDROLASE INHIBITOR COMPLEX, SERINE PROTEINASE
H
SER
36
B
SER
22
A
1
H
PRO
37
B
PRO
23
-0.59
THRB_HUMAN
UNP
1
328
P00734
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
THRB_HUMAN
UNP
2
364
P00734
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISM
LEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL
QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE
HIR3A_HIRME
UNP
3
55
P28507
DFEEIPEEYLQ
328
363
1DWE
1
14
P00734
H
N
L
1
1
36
364
622
1DWE
16
247
P00734
H
2
1
259
55
65
1DWE
1
11
P28507
I
3
1
11
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
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
SER
48
B
SER
34
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
BINDING SITE FOR RESIDUE 0G6 H 1
Software
17
BINDING SITE FOR CHAIN I OF HIRUDIN IIIA
Software
20
H
HIS
57
B
HIS
43
17
1_555
H
TYR
60
B
TYR
47
A
17
1_555
H
TRP
60
B
TRP
50
D
17
1_555
H
ILE
174
B
ILE
179
17
1_555
H
ASP
189
B
ASP
199
17
1_555
H
ALA
190
B
ALA
200
17
1_555
H
GLU
192
B
GLU
202
17
1_555
H
GLY
193
B
GLY
203
17
1_555
H
SER
195
B
SER
205
17
1_555
H
SER
214
B
SER
226
17
1_555
H
TRP
215
B
TRP
227
17
1_555
H
GLY
216
B
GLY
228
17
1_555
H
GLY
219
B
GLY
230
17
1_555
H
HOH
293
F
HOH
17
1_555
H
HOH
294
F
HOH
17
1_555
H
HOH
295
F
HOH
17
1_555
H
HOH
296
F
HOH
17
1_555
H
LYS
36
B
LYS
21
20
1_555
H
GLN
38
B
GLN
24
20
1_555
H
ARG
73
B
ARG
68
20
1_555
H
THR
74
B
THR
69
20
1_555
H
ARG
75
B
ARG
70
20
1_555
H
ARG
75
B
ARG
70
20
7_555
H
TYR
76
B
TYR
71
20
1_555
H
ILE
82
B
ILE
78
20
1_555
H
HIS
91
B
HIS
87
20
3_544
H
ARG
101
B
ARG
98
20
3_544
H
ARG
233
B
ARG
245
20
3_544
H
LEU
234
B
LEU
246
20
3_544
H
LYS
236
B
LYS
248
20
3_544
H
TRP
237
B
TRP
249
20
3_544
H
GLN
239
B
GLN
251
20
3_544
H
LYS
240
B
LYS
252
20
3_544
H
HOH
251
F
HOH
20
1_555
I
HOH
16
G
HOH
20
1_555
I
HOH
17
G
HOH
20
1_555
I
HOH
19
G
HOH
20
7_555
96
P 43 21 2