Structure of PDB 3si4 Chain H Binding Site BS03

Receptor Information
>3si4 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 IDB04
InChIInChI=1S/C21H26N4O2/c1-24-12-6-5-10-17(24)15-23-20(26)19-11-7-13-25(19)21(27)18(22)14-16-8-3-2-4-9-16/h2-6,8-10,12,18-19H,7,11,13-15,22H2,1H3/p+1/t18-,19+/m1/s1
InChIKeyGWFYERFSYVJQNW-MOPGFXCFSA-O
SMILES
SoftwareSMILES
CACTVS 3.370C[n+]1ccccc1CNC(=O)[C@@H]2CCCN2C(=O)[C@H](N)Cc3ccccc3
OpenEye OEToolkits 1.7.2C[n+]1ccccc1CNC(=O)C2CCCN2C(=O)C(Cc3ccccc3)N
OpenEye OEToolkits 1.7.2C[n+]1ccccc1CNC(=O)[C@@H]2CCCN2C(=O)[C@@H](Cc3ccccc3)N
ACDLabs 12.01O=C(NCc1[n+](cccc1)C)C3N(C(=O)C(N)Cc2ccccc2)CCC3
CACTVS 3.370C[n+]1ccccc1CNC(=O)[CH]2CCCN2C(=O)[CH](N)Cc3ccccc3
FormulaC21 H27 N4 O2
NameD-phenylalanyl-N-[(1-methylpyridinium-2-yl)methyl]-L-prolinamide
ChEMBL
DrugBank
ZINCZINC000098208688
PDB chain3si4 Chain H Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3si4 Impact of ligand and protein desolvation on ligand binding to the S1 pocket of thrombin
Resolution1.27 Å
Binding residue
(original residue number in PDB)		Y60A W60D N98 V213 S214 W215 G216
Binding residue
(residue number reindexed from 1)		Y47 W50 N95 V218 S219 W220 G221
Annotation score1
Binding affinityMOAD: Ki=132.2uM
PDBbind-CN: -logKd/Ki=3.88,Ki=132.2uM
Enzymatic activity
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:3si4, PDBe:3si4, PDBj:3si4
PDBsum3si4
PubMed22366545
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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