Structure of PDB 4ufg Chain H Binding Site BS03

Receptor Information
>4ufg 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 IDD6J
InChIInChI=1S/C29H35N5O4S/c1-3-26(28(35)32-19-22-14-16-24(17-15-22)27(30)31)34(2)29(36)25(18-21-10-6-4-7-11-21)33-39(37,38)20-23-12-8-5-9-13-23/h4-17,25-26,33H,3,18-20H2,1-2H3,(H3,30,31)(H,32,35)/t25-,26+/m1/s1
InChIKeyOVCZZMWCFCLIPI-FTJBHMTQSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC[C@H](N(C)C(=O)[C@@H](Cc1ccccc1)N[S](=O)(=O)Cc2ccccc2)C(=O)NCc3ccc(cc3)C(N)=N
CACTVS 3.385CC[CH](N(C)C(=O)[CH](Cc1ccccc1)N[S](=O)(=O)Cc2ccccc2)C(=O)NCc3ccc(cc3)C(N)=N
OpenEye OEToolkits 1.7.6CCC(C(=O)NCc1ccc(cc1)C(=N)N)N(C)C(=O)C(Cc2ccccc2)NS(=O)(=O)Cc3ccccc3
OpenEye OEToolkits 1.7.6CC[C@@H](C(=O)NCc1ccc(cc1)C(=N)N)N(C)C(=O)[C@@H](Cc2ccccc2)NS(=O)(=O)Cc3ccccc3
FormulaC29 H35 N5 O4 S
Name(2S)-N-[(4-carbamimidoylphenyl)methyl]-2-[methyl-[(2R)-3-phenyl-2-[(phenylmethyl)sulfonylamino]propanoyl]amino]butanamide
ChEMBL
DrugBank
ZINCZINC000263620862
PDB chain4ufg Chain H Residue 1249 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ufg 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.
Resolution1.65 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D N98 L99 I174 D189 A190 E192 S195 V213 S214 W215 G216 E217 G219
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 N95 L96 I172 D192 A193 E195 S198 V218 S219 W220 G221 E222 G223
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.15,Ki=7nM
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:4ufg, PDBe:4ufg, PDBj:4ufg
PDBsum4ufg
PubMed26762840
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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