Structure of PDB 3qtv Chain H Binding Site BS03

Receptor Information
>3qtv 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 ID06P
InChIInChI=1S/C21H26N4O2/c1-24-12-9-17(10-13-24)15-23-20(26)19-8-5-11-25(19)21(27)18(22)14-16-6-3-2-4-7-16/h2-4,6-7,9-10,12-13,18-19H,5,8,11,14-15,22H2,1H3/p+1/t18-,19+/m1/s1
InChIKeyXPNLMZJVXKGMFM-MOPGFXCFSA-O
SMILES
SoftwareSMILES
CACTVS 3.370C[n+]1ccc(CNC(=O)[CH]2CCCN2C(=O)[CH](N)Cc3ccccc3)cc1
CACTVS 3.370C[n+]1ccc(CNC(=O)[C@@H]2CCCN2C(=O)[C@H](N)Cc3ccccc3)cc1
ACDLabs 12.01O=C(NCc1cc[n+](cc1)C)C3N(C(=O)C(N)Cc2ccccc2)CCC3
OpenEye OEToolkits 1.7.0C[n+]1ccc(cc1)CNC(=O)C2CCCN2C(=O)C(Cc3ccccc3)N
OpenEye OEToolkits 1.7.0C[n+]1ccc(cc1)CNC(=O)[C@@H]2CCCN2C(=O)[C@@H](Cc3ccccc3)N
FormulaC21 H27 N4 O2
NameD-phenylalanyl-N-[(1-methylpyridinium-4-yl)methyl]-L-prolinamide
ChEMBL
DrugBank
ZINCZINC000095920602
PDB chain3qtv Chain H Residue 1001 [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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PDB3qtv Impact of ligand and protein desolvation on ligand binding to the S1 pocket of thrombin
Resolution1.63 Å
Binding residue
(original residue number in PDB)		Y60A W60D D189 E192 S195 S214 W215 G216 G219
Binding residue
(residue number reindexed from 1)		Y47 W50 D192 E195 S198 S219 W220 G221 G223
Annotation score1
Binding affinityMOAD: Ki=22.5uM
PDBbind-CN: -logKd/Ki=4.65,Ki=22.5uM
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:3qtv, PDBe:3qtv, PDBj:3qtv
PDBsum3qtv
PubMed22366545
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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