Structure of PDB 3sha Chain H Binding Site BS03

Receptor Information
>3sha 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 IDP97
InChIInChI=1S/C20H23ClN4O2/c21-16-8-9-23-12-15(16)13-24-19(26)18-7-4-10-25(18)20(27)17(22)11-14-5-2-1-3-6-14/h1-3,5-6,8-9,12,17-18H,4,7,10-11,13,22H2,(H,24,26)/t17-,18+/m1/s1
InChIKeyZRBVLANXQQYBLM-MSOLQXFVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2c1ccc(cc1)C[C@H](C(=O)N2CCC[C@H]2C(=O)NCc3cnccc3Cl)N
OpenEye OEToolkits 1.7.2c1ccc(cc1)CC(C(=O)N2CCCC2C(=O)NCc3cnccc3Cl)N
CACTVS 3.370N[CH](Cc1ccccc1)C(=O)N2CCC[CH]2C(=O)NCc3cnccc3Cl
CACTVS 3.370N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3cnccc3Cl
ACDLabs 12.01O=C(NCc1c(Cl)ccnc1)C3N(C(=O)C(N)Cc2ccccc2)CCC3
FormulaC20 H23 Cl N4 O2
NameD-phenylalanyl-N-[(4-chloropyridin-3-yl)methyl]-L-prolinamide
ChEMBL
DrugBank
ZINCZINC000095920845
PDB chain3sha Chain H Residue 1 [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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PDB3sha Impact of ligand and protein desolvation on ligand binding to the S1 pocket of thrombin
Resolution1.52 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D L99 I174 S195 S214 W215 G216
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 L96 I172 S198 S219 W220 G221
Annotation score1
Binding affinityMOAD: Ki=2.6uM
PDBbind-CN: -logKd/Ki=5.59,Ki=2.6uM
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:3sha, PDBe:3sha, PDBj:3sha
PDBsum3sha
PubMed22366545
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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