Structure of PDB 4uff Chain H Binding Site BS03

Receptor Information
>4uff Chain H (length=250) 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
Ligand information
Ligand ID6V2
InChIInChI=1S/C27H31N5O4S/c1-32(18-25(33)30-17-21-12-14-23(15-13-21)26(28)29)27(34)24(16-20-8-4-2-5-9-20)31-37(35,36)19-22-10-6-3-7-11-22/h2-15,24,31H,16-19H2,1H3,(H3,28,29)(H,30,33)/t24-/m1/s1
InChIKeyYUCRZSXJDNYWCT-XMMPIXPASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CN(CC(=O)NCc1ccc(cc1)C(=N)N)C(=O)C(Cc2ccccc2)NS(=O)(=O)Cc3ccccc3
CACTVS 3.385CN(CC(=O)NCc1ccc(cc1)C(N)=N)C(=O)[C@@H](Cc2ccccc2)N[S](=O)(=O)Cc3ccccc3
OpenEye OEToolkits 1.7.6[H]/N=C(\c1ccc(cc1)CNC(=O)CN(C)C(=O)[C@@H](Cc2ccccc2)NS(=O)(=O)Cc3ccccc3)/N
CACTVS 3.385CN(CC(=O)NCc1ccc(cc1)C(N)=N)C(=O)[CH](Cc2ccccc2)N[S](=O)(=O)Cc3ccccc3
FormulaC27 H31 N5 O4 S
Name(2R)-2-(benzylsulfonylamino)-N-(2-((4-carbamimidoylphenyl)methylamino)-2-oxo-ethyl)-N-methyl-3-phenyl-propanamide
ChEMBL
DrugBank
ZINCZINC000263621308
PDB chain4uff Chain H Residue 1248 [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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PDB4uff Boosting Affinity by Correct Ligand Preorganization for the S2 Pocket of Thrombin: A Study by Isothermal Titration Calorimetry, Molecular Dynamics, and High-Resolution Crystal Structures.
Resolution1.55 Å
Binding residue
(original residue number in PDB)		Y60A W60D N98 L99 D189 A190 S195 V213 S214 W215 G216 E217 G219 C220
Binding residue
(residue number reindexed from 1)		Y47 W50 N95 L96 D192 A193 S198 V218 S219 W220 G221 E222 G223 C224
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.96,Ki=11nM
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:4uff, PDBe:4uff, PDBj:4uff
PDBsum4uff
PubMed26762840
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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