Structure of PDB 6yhj Chain H Binding Site BS03

Receptor Information
>6yhj Chain H (length=253) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWKG
QPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDS
GGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVID
QFG
Ligand information
Ligand IDOQZ
InChIInChI=1S/C19H22ClN3O2S/c20-17-9-8-14(26-17)12-22-18(24)16-7-4-10-23(16)19(25)15(21)11-13-5-2-1-3-6-13/h1-3,5-6,8-9,15-16H,4,7,10-12,21H2,(H,22,24)/t15-,16+/m1/s1
InChIKeyRAMUDOPEEQUPEA-CVEARBPZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc(cc1)C[C@H](C(=O)N2CCC[C@H]2C(=O)NCc3ccc(s3)Cl)N
OpenEye OEToolkits 2.0.7c1ccc(cc1)CC(C(=O)N2CCCC2C(=O)NCc3ccc(s3)Cl)N
CACTVS 3.385N[CH](Cc1ccccc1)C(=O)N2CCC[CH]2C(=O)NCc3sc(Cl)cc3
CACTVS 3.385N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3sc(Cl)cc3
FormulaC19 H22 Cl N3 O2 S
Name(2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(5-chloranylthiophen-2-yl)methyl]pyrrolidine-2-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain6yhj Chain H Residue 306 [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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PDB6yhj Thrombin in complex with D-Phe-Pro-2-chlorothiophen derivative (16e)
Resolution1.44 Å
Binding residue
(original residue number in PDB)
Y60A N98 C191 S214 W215 G216
Binding residue
(residue number reindexed from 1)
Y47 N95 C196 S221 W222 G223
Annotation score1
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 E197 G198 D199 S200 G201
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:6yhj, PDBe:6yhj, PDBj:6yhj
PDBsum6yhj
PubMed
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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