Structure of PDB 4ufd Chain H Binding Site BS03

Receptor Information
>4ufd 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 IDS49
InChIInChI=1S/C29H33N5O4S/c30-27(31)24-15-13-22(14-16-24)19-32-28(35)26-12-7-17-34(26)29(36)25(18-21-8-3-1-4-9-21)33-39(37,38)20-23-10-5-2-6-11-23/h1-6,8-11,13-16,25-26,33H,7,12,17-20H2,(H3,30,31)(H,32,35)/t25-,26+/m1/s1
InChIKeyVAMQUIIDPUWWSK-FTJBHMTQSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC(=N)c1ccc(CNC(=O)[C@@H]2CCCN2C(=O)[C@@H](Cc3ccccc3)N[S](=O)(=O)Cc4ccccc4)cc1
ACDLabs 12.01C(S(=O)(=O)NC(Cc1ccccc1)C(N3C(C(=O)NCc2ccc(/C(N)=N)cc2)CCC3)=O)c4ccccc4
OpenEye OEToolkits 1.7.6[H]/N=C(/c1ccc(cc1)CNC(=O)[C@@H]2CCCN2C(=O)[C@@H](Cc3ccccc3)NS(=O)(=O)Cc4ccccc4)\N
CACTVS 3.385NC(=N)c1ccc(CNC(=O)[CH]2CCCN2C(=O)[CH](Cc3ccccc3)N[S](=O)(=O)Cc4ccccc4)cc1
OpenEye OEToolkits 1.7.6c1ccc(cc1)CC(C(=O)N2CCCC2C(=O)NCc3ccc(cc3)C(=N)N)NS(=O)(=O)Cc4ccccc4
FormulaC29 H33 N5 O4 S
Name(2S)-N-[(4-carbamimidoylphenyl)methyl]-1-[(2R)-3-phenyl-2-[(phenylmethyl)sulfonylamino]propanoyl]pyrrolidine-2-carboxamide
ChEMBLCHEMBL1809220
DrugBank
ZINCZINC000072178453
PDB chain4ufd Chain H Residue 1251 [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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PDB4ufd 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.
Resolution1.429 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D N98 L99 D189 A190 E192 V213 S214 W215 G216 G219 C220
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 N95 L96 D192 A193 E195 V218 S219 W220 G221 G223 C224
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.68,Ki=0.21nM
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
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Biological Process
External links
PDB RCSB:4ufd, PDBe:4ufd, PDBj:4ufd
PDBsum4ufd
PubMed26762840
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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