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1C5Y
Asym. Unit
Info
Asym.Unit (113 KB)
Biol.Unit 1 (107 KB)
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Title
:
STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, SUB-MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR
Authors
:
B. A. Katz, R. Mackman, C. Luong, K. Radika, A. Martelli, P. A. Sprengeler, J. Wang, H. Chan, L. Wong
Date
:
22 Dec 99 (Deposition) - 22 Dec 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Selective, S1 Site Inhibitor, Structure-Based Drug Design, Urokinase, Trypsin, Thrombin, Blood Clotting
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. A. Katz, R. Mackman, C. Luong, K. Radika, A. Martelli, P. A. Sprengeler, J. Wang, H. Chan, L. Wong
Structural Basis For Selectivity Of A Small Molecule, S1-Binding, Submicromolar Inhibitor Of Urokinase-Type Plasminogen Activator.
Chem. Biol. V. 7 299 2000
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: THIENO[2,3-B]PYRIDINE-2-CARBOXAMID... (ESPa)
2a: CITRATE ANION (FLCa)
2b: CITRATE ANION (FLCb)
2c: CITRATE ANION (FLCc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ESP
1
Ligand/Ion
THIENO[2,3-B]PYRIDINE-2-CARBOXAMIDINE
2
FLC
3
Ligand/Ion
CITRATE ANION
[
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]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR B:67 , LYS B:82 , SER B:164 , HIS B:165 , ARG B:166 , HOH B:276 , HOH B:400 , HOH B:529 , HOH B:534
BINDING SITE FOR RESIDUE FLC B 1
2
AC2
SOFTWARE
ARG B:36 , LYS B:82 , LYS B:110A , HIS B:165 , ARG B:230 , HOH B:400 , HOH B:498 , HOH B:534
BINDING SITE FOR RESIDUE FLC B 2
3
AC3
SOFTWARE
HIS B:57 , HIS B:99 , GLN B:192 , GLY B:193 , SER B:195 , ESP B:251 , HOH B:285 , HOH B:406 , HOH B:489 , HOH B:560 , HOH B:561 , HOH B:562
BINDING SITE FOR RESIDUE FLC B 3
4
AC4
SOFTWARE
FLC B:3 , ASP B:189 , SER B:190 , GLN B:192 , SER B:195 , TRP B:215 , GLY B:216 , GLY B:219 , CYS B:220 , GLY B:226 , HOH B:485 , HOH B:487
BINDING SITE FOR RESIDUE ESP B 251
[
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SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_013102 (M47M, chain B, )
2: VAR_038731 (K61Q, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_013102
I
214
M
UROK_HUMAN
Polymorphism
---
B
M
47
M
2
UniProt
VAR_038731
K
231
Q
UROK_HUMAN
Polymorphism
2227567
B
K
61
Q
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: TRYPSIN_DOM (B:16-243)
2: TRYPSIN_HIS (B:53-58)
3: TRYPSIN_SER (B:189-200)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TRYPSIN_DOM
PS50240
Serine proteases, trypsin domain profile.
UROK_HUMAN
179-424
1
B:16-243
2
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
UROK_HUMAN
220-225
1
B:53-58
3
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
UROK_HUMAN
370-381
1
B:189-200
[
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Exons
(5, 6)
Info
All Exons
Exon 1.9b (A:9-17 | B:16-60)
Exon 1.10 (- | B:60-104)
Exon 1.11 (- | B:104-147)
Exon 1.13 (- | B:147-192)
Exon 1.14d (- | B:193-245 (gaps))
View:
Select:
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All Exon Boundaries
1: Boundary 1.8/1.9b
2: Boundary 1.9b/1.10
3: Boundary 1.10/1.11
4: Boundary 1.11/1.13
5: Boundary 1.13/1.14d
6: Boundary 1.14d/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.3c
ENST00000372764
3c
ENSE00001820360
chr10:
75670915-75670976
62
UROK_HUMAN
-
0
0
-
-
1.4b
ENST00000372764
4b
ENSE00002193721
chr10:
75671283-75671370
88
UROK_HUMAN
1-19
19
0
-
-
1.5
ENST00000372764
5
ENSE00001276413
chr10:
75671799-75671826
28
UROK_HUMAN
20-29
10
0
-
-
1.6a
ENST00000372764
6a
ENSE00001169210
chr10:
75671973-75672080
108
UROK_HUMAN
29-65
37
0
-
-
1.7b
ENST00000372764
7b
ENSE00001169200
chr10:
75672682-75672856
175
UROK_HUMAN
65-123
59
0
-
-
1.8
ENST00000372764
8
ENSE00000834105
chr10:
75673048-75673139
92
UROK_HUMAN
123-154
32
0
-
-
1.9b
ENST00000372764
9b
ENSE00001169184
chr10:
75673297-75673516
220
UROK_HUMAN
154-227
74
2
A:9-17
B:16-60
9
49
1.10
ENST00000372764
10
ENSE00001169178
chr10:
75673738-75673886
149
UROK_HUMAN
227-277
51
1
-
B:60-104
-
51
1.11
ENST00000372764
11
ENSE00001169173
chr10:
75674534-75674674
141
UROK_HUMAN
277-324
48
1
-
B:104-147
-
48
1.13
ENST00000372764
13
ENSE00001169164
chr10:
75675009-75675157
149
UROK_HUMAN
324-373
50
1
-
B:147-192
-
50
1.14d
ENST00000372764
14d
ENSE00001892698
chr10:
75676147-75677255
1109
UROK_HUMAN
374-431
58
1
-
B:193-245 (gaps)
-
54
[
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SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1c5y_1 (A:,B:)
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Protein Domains
(
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(
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Organisms
(
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(
)
Class
:
All beta proteins
(24004)
Fold
:
Trypsin-like serine proteases
(1752)
Superfamily
:
Trypsin-like serine proteases
(1752)
Family
:
Eukaryotic proteases
(1343)
Protein domain
:
Urokinase-type plasminogen activator (LMW U-PA), catalytic domain
(66)
Human (Homo sapiens) [TaxId: 9606]
(66)
1a
d1c5y.1
A:,B:
[
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1c5yB02 (B:28-120,B:233-245)
1b: CATH_1c5yB01 (B:16-27,B:121-232)
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(
)
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)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Thrombin, subunit H
(1535)
Homologous Superfamily
:
Trypsin-like serine proteases
(1488)
Human (Homo sapiens)
(615)
1a
1c5yB02
B:28-120,B:233-245
1b
1c5yB01
B:16-27,B:121-232
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asymmetric Unit 1
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Asym.Unit (113 KB)
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