Structure of PDB 6t3m Chain H Binding Site BS03

Receptor Information
>6t3m Chain H (length=251) 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
G
Ligand information
Ligand IDMD8
InChIInChI=1S/C21H25N3O3/c22-18(13-15-5-2-1-3-6-15)21(27)24-12-4-7-19(24)20(26)23-14-16-8-10-17(25)11-9-16/h1-3,5-6,8-11,18-19,25H,4,7,12-14,22H2,(H,23,26)/t18-,19+/m1/s1
InChIKeyFQTMKKZTHOHYNU-MOPGFXCFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc(cc1)CC(C(=O)N2CCCC2C(=O)NCc3ccc(cc3)O)N
CACTVS 3.385N[CH](Cc1ccccc1)C(=O)N2CCC[CH]2C(=O)NCc3ccc(O)cc3
CACTVS 3.385N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3ccc(O)cc3
OpenEye OEToolkits 2.0.7c1ccc(cc1)C[C@H](C(=O)N2CCC[C@H]2C(=O)NCc3ccc(cc3)O)N
FormulaC21 H25 N3 O3
Name(2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(4-hydroxyphenyl)methyl]pyrrolidine-2-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain6t3m Chain H Residue 303 [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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PDB6t3m Thrombin in Complex with a D-Phe-Pro-p-phenol derivative
Resolution1.38 Å
Binding residue
(original residue number in PDB)		I47 L123 P124 K235 I238
Binding residue
(residue number reindexed from 1)		I33 L120 P121 K240 I243
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 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:6t3m, PDBe:6t3m, PDBj:6t3m
PDBsum6t3m
PubMed
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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