Structure of PDB 3si3 Chain H Binding Site BS03

Receptor Information
>3si3 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 IDB03
InChIInChI=1S/C20H24N4O2/c21-17(13-15-7-2-1-3-8-15)20(26)24-12-6-10-18(24)19(25)23-14-16-9-4-5-11-22-16/h1-5,7-9,11,17-18H,6,10,12-14,21H2,(H,23,25)/t17-,18+/m1/s1
InChIKeyBUZZZPBDSHVEFR-MSOLQXFVSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(NCc1ncccc1)C3N(C(=O)C(N)Cc2ccccc2)CCC3
OpenEye OEToolkits 1.7.2c1ccc(cc1)CC(C(=O)N2CCCC2C(=O)NCc3ccccn3)N
CACTVS 3.370N[CH](Cc1ccccc1)C(=O)N2CCC[CH]2C(=O)NCc3ccccn3
OpenEye OEToolkits 1.7.2c1ccc(cc1)C[C@H](C(=O)N2CCC[C@H]2C(=O)NCc3ccccn3)N
CACTVS 3.370N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3ccccn3
FormulaC20 H24 N4 O2
NameD-phenylalanyl-N-(pyridin-2-ylmethyl)-L-prolinamide
ChEMBL
DrugBank
ZINCZINC000098208687
PDB chain3si3 Chain H Residue 5 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3si3 Impact of ligand and protein desolvation on ligand binding to the S1 pocket of thrombin
Resolution1.55 Å
Binding residue
(original residue number in PDB)		Y60A W60D N98 L99 I174 V213 S214 W215 G216
Binding residue
(residue number reindexed from 1)		Y47 W50 N95 L96 I172 V218 S219 W220 G221
Annotation score1
Binding affinityMOAD: Ki=69.3uM
PDBbind-CN: -logKd/Ki=4.16,Ki=69.3uM
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:3si3, PDBe:3si3, PDBj:3si3
PDBsum3si3
PubMed22366545
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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