Structure of PDB 4ayv Chain B Binding Site BS02

Receptor Information
>4ayv Chain B (length=257) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTA
NVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDA
CEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWI
QKVIDQF
Ligand information
Ligand ID9MQ
InChIInChI=1S/C30H36N6O6S/c31-30(32)35-14-6-9-22(19-35)17-33-27(37)16-26(29(40)36(20-28(38)39)18-21-7-2-1-3-8-21)34-43(41,42)25-13-12-23-10-4-5-11-24(23)15-25/h1-5,7-8,10-13,15,22,26,34H,6,9,14,16-20H2,(H3,31,32)(H,33,37)(H,38,39)/t22-,26-/m0/s1
InChIKeyZWJYDBRLGHLMKT-NVQXNPDNSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)CN(C(=O)C(NS(=O)(=O)c2cc1ccccc1cc2)CC(=O)NCC3CCCN(C(=[N@H])N)C3)Cc4ccccc4
CACTVS 3.385NC(=N)N1CCC[CH](CNC(=O)C[CH](N[S](=O)(=O)c2ccc3ccccc3c2)C(=O)N(CC(O)=O)Cc4ccccc4)C1
OpenEye OEToolkits 1.9.2[H]/N=C(\N)/N1CCC[C@H](C1)CNC(=O)C[C@@H](C(=O)N(Cc2ccccc2)CC(=O)O)NS(=O)(=O)c3ccc4ccccc4c3
OpenEye OEToolkits 1.9.2c1ccc(cc1)CN(CC(=O)O)C(=O)C(CC(=O)NCC2CCCN(C2)C(=N)N)NS(=O)(=O)c3ccc4ccccc4c3
CACTVS 3.385NC(=N)N1CCC[C@@H](CNC(=O)C[C@H](N[S](=O)(=O)c2ccc3ccccc3c2)C(=O)N(CC(O)=O)Cc4ccccc4)C1
FormulaC30 H36 N6 O6 S
Name{Benzyl-[(S)-3-[((S)-1-carbamimidoyl-piperidin-3-ylmethyl)-carbamoyl]-2-(naphthalene-2-sulfonylamino)-propionyl]-amino}-acetic acid
ChEMBLCHEMBL341260
DrugBank
ZINCZINC000027305405
PDB chain4ayv Chain B Residue 1258 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4ayv Design and Synthesis of Potent and Highly Selective Thrombin Inhibitors.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		H43 Y47 I179 D199 S205 V225 W227 G228 E229 G230
Binding residue
(residue number reindexed from 1)		H43 Y47 I179 D199 S205 V225 W227 G228 E229 G230
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.17,Ki=0.68nM
BindingDB: Ki=0.68nM
Enzymatic activity
Catalytic site (original residue number in PDB) H43 D99 E202 G203 D204 S205 G206
Catalytic site (residue number reindexed from 1) H43 D99 E202 G203 D204 S205 G206
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:4ayv, PDBe:4ayv, PDBj:4ayv
PDBsum4ayv
PubMed7966150
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

[Back to BioLiP]