Structure of PDB 6t4a Chain H Binding Site BS03

Receptor Information
>6t4a 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 IDJ5K
InChIInChI=1S/C20H25N5O2/c21-16(11-14-5-2-1-3-6-14)20(27)25-10-4-7-17(25)19(26)24-13-15-8-9-18(22)23-12-15/h1-3,5-6,8-9,12,16-17H,4,7,10-11,13,21H2,(H2,22,23)(H,24,26)/t16-,17+/m1/s1
InChIKeyIWAABGNHPAYUJJ-SJORKVTESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc(cc1)CC(C(=O)N2CCCC2C(=O)NCc3ccc(nc3)N)N
CACTVS 3.385N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3ccc(N)nc3
OpenEye OEToolkits 2.0.6c1ccc(cc1)C[C@H](C(=O)N2CCC[C@H]2C(=O)NCc3ccc(nc3)N)N
CACTVS 3.385N[CH](Cc1ccccc1)C(=O)N2CCC[CH]2C(=O)NCc3ccc(N)nc3
FormulaC20 H25 N5 O2
Name(2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(6-azanylpyridin-3-yl)methyl]pyrrolidine-2-carboxamide;
D-Phe-Pro-p-aminopyridine
ChEMBLCHEMBL4597222
DrugBank
ZINC
PDB chain6t4a Chain H Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6t4a Protein-Induced Change in Ligand Protonation during Trypsin and Thrombin Binding: Hint on Differences in Selectivity Determinants of Both Proteins?
Resolution1.31 Å
Binding residue
(original residue number in PDB)		Y60A W60D L99 A190 E192 S195 S214 W215 G216 G219 C220
Binding residue
(residue number reindexed from 1)		Y47 W50 L96 A193 E195 S198 S219 W220 G221 G223 C224
Annotation score1
Binding affinityMOAD: 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:6t4a, PDBe:6t4a, PDBj:6t4a
PDBsum6t4a
PubMed32011145
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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