Structure of PDB 4ayy Chain B Binding Site BS02

Receptor Information
>4ayy 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 ID9MX
InChIInChI=1S/C28H38N6O6S/c1-18-10-12-34(24(13-18)27(37)38)26(36)23(15-25(35)31-16-19-5-4-11-33(17-19)28(29)30)32-41(39,40)22-9-8-20-6-2-3-7-21(20)14-22/h2-3,6-9,14,18-19,23-24,32H,4-5,10-13,15-17H2,1H3,(H3,29,30)(H,31,35)(H,37,38)/t18-,19+,23+,24-/m1/s1
InChIKeyBPPNPBQJRWCUDE-RJADORODSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC1CCN(C(C1)C(=O)O)C(=O)C(CC(=O)NCC2CCCN(C2)C(=N)N)NS(=O)(=O)c3ccc4ccccc4c3
CACTVS 3.370C[C@@H]1CCN([C@H](C1)C(O)=O)C(=O)[C@H](CC(=O)NC[C@@H]2CCCN(C2)C(N)=N)N[S](=O)(=O)c3ccc4ccccc4c3
OpenEye OEToolkits 1.7.6[H]/N=C(/N)\N1CCC[C@H](C1)CNC(=O)C[C@@H](C(=O)N2CC[C@H](C[C@@H]2C(=O)O)C)NS(=O)(=O)c3ccc4ccccc4c3
ACDLabs 12.01O=C(N1C(C(=O)O)CC(C)CC1)C(NS(=O)(=O)c3cc2ccccc2cc3)CC(=O)NCC4CCCN(C(=[N@H])N)C4
CACTVS 3.370C[CH]1CCN([CH](C1)C(O)=O)C(=O)[CH](CC(=O)NC[CH]2CCCN(C2)C(N)=N)N[S](=O)(=O)c3ccc4ccccc4c3
FormulaC28 H38 N6 O6 S
Name(R)-1-[(S)-3-[((S)-1-Carbamimidoyl-piperidin-3-ylmethyl)-carbamoyl]-2-(naphthalene-2-sulfonylamino)-propionyl]-4-methyl-piperidine-2-carboxylic acid
ChEMBLCHEMBL126238
DrugBank
ZINCZINC000027307653
PDB chain4ayy 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

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PDB4ayy Design and Synthesis of Potent and Highly Selective Thrombin Inhibitors.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		H43 Y47 W50 L96 D199 C201 W227 G228 G230
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 L96 D199 C201 W227 G228 G230
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.17,Ki=6.7nM
BindingDB: Ki=6.7nM
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

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4ayy, PDBe:4ayy, PDBj:4ayy
PDBsum4ayy
PubMed7966150
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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