Structure of PDB 1g30 Chain B Binding Site BS03

Receptor Information
>1g30 Chain B (length=252) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF
GE
Ligand information
Ligand IDT87
InChIInChI=1S/C29H31N7O3/c1-3-38-26(37)18-39-35-27(22-6-4-5-15-32-22)29(13-14-29)20-9-12-24-23(16-20)34-25(36(24)2)17-33-21-10-7-19(8-11-21)28(30)31/h4-12,15-16,33H,3,13-14,17-18H2,1-2H3,(H3,30,31)/b35-27-
InChIKeyRNOYCNIZOAIUSV-LSWMGQQCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0[H]/N=C(/c1ccc(cc1)NCc2nc3cc(ccc3n2C)C4(CC4)/C(=N\OCC(=O)OCC)/c5ccccn5)\N
ACDLabs 10.04O=C(OCC)CO\N=C(\c1ncccc1)C5(c4ccc2c(nc(n2C)CNc3ccc(C(=[N@H])N)cc3)c4)CC5
CACTVS 3.341CCOC(=O)CO\N=C(c1ccccn1)/C2(CC2)c3ccc4n(C)c(CNc5ccc(cc5)C(N)=N)nc4c3
CACTVS 3.341CCOC(=O)CON=C(c1ccccn1)C2(CC2)c3ccc4n(C)c(CNc5ccc(cc5)C(N)=N)nc4c3
OpenEye OEToolkits 1.5.0[H]N=C(c1ccc(cc1)NCc2nc3cc(ccc3n2C)C4(CC4)C(=NOCC(=O)OCC)c5ccccn5)N
FormulaC29 H31 N7 O3
Name[(1-{2[(4-CARBAMIMIDOYL-PHENYLAMINO)-METHYL]-1-METHYL-1H-BENZOIMIDAZOL-5-YL}-CYCLOPROPYL)-PYRIDIN-2-YL-METHYLENEAMINOOXY]-ACETIC ACID ETHYL ESTER
ChEMBL
DrugBankDB04107
ZINCZINC000006409740
PDB chain1g30 Chain B Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1g30 Structural basis for inhibition promiscuity of dual specific thrombin and factor Xa blood coagulation inhibitors.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D N98 L99 I174 D189 A190 S195 V213 S214 W215 G216
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 N95 L96 I172 D192 A193 S198 V218 S219 W220 G221
Annotation score1
Binding affinityMOAD: Ki=140nM
PDBbind-CN: -logKd/Ki=6.85,Ki=140nM
BindingDB: Ki=140nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 E192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H43 D99 E195 G196 D197 S198 G199
Enzyme Commision number 3.4.21.5: thrombin.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
GO:0005509 calcium ion binding
Biological Process
GO:0006508 proteolysis
GO:0007596 blood coagulation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1g30, PDBe:1g30, PDBj:1g30
PDBsum1g30
PubMed11342132
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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