Structure of PDB 3da9 Chain B Binding Site BS03

Receptor Information
>3da9 Chain B (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 ID44U
InChIInChI=1S/C23H29N3O2/c1-2-15-25-22(27)19-14-9-16-26(19)23(28)21(24)20(17-10-5-3-6-11-17)18-12-7-4-8-13-18/h3-8,10-13,19-21H,2,9,14-16,24H2,1H3,(H,25,27)/t19-,21+/m0/s1
InChIKeyHZKKJPDVZGOOPU-PZJWPPBQSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCCNC(=O)[CH]1CCCN1C(=O)[CH](N)C(c2ccccc2)c3ccccc3
CACTVS 3.341CCCNC(=O)[C@@H]1CCCN1C(=O)[C@H](N)C(c2ccccc2)c3ccccc3
OpenEye OEToolkits 1.5.0CCCNC(=O)[C@@H]1CCCN1C(=O)[C@@H](C(c2ccccc2)c3ccccc3)N
OpenEye OEToolkits 1.5.0CCCNC(=O)C1CCCN1C(=O)C(C(c2ccccc2)c3ccccc3)N
ACDLabs 10.04O=C(NCCC)C3N(C(=O)C(N)C(c1ccccc1)c2ccccc2)CCC3
FormulaC23 H29 N3 O2
Namebeta-phenyl-D-phenylalanyl-N-propyl-L-prolinamide
ChEMBLCHEMBL490730
DrugBankDB07083
ZINCZINC000039115027
PDB chain3da9 Chain B Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3da9 Compounds binding to the S2-S3 pockets of thrombin.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		Y83 N131 L132 I209 C231 S235 S256 W257 G258 E259
Binding residue
(residue number reindexed from 1)		Y47 N95 L96 I172 C194 S198 S219 W220 G221 E222
Annotation score1
Binding affinityMOAD: Kd=3.1uM
PDBbind-CN: -logKd/Ki=5.51,Kd=3.1uM
BindingDB: Kd=3100nM,IC50=18000nM
Enzymatic activity
Catalytic site (original residue number in PDB) H79 D135 E232 G233 D234 S235 G236
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:3da9, PDBe:3da9, PDBj:3da9
PDBsum3da9
PubMed19371038
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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