Structure of PDB 4udw Chain H Binding Site BS03

Receptor Information
>4udw 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 IDN6L
InChIInChI=1S/C21H23Cl2N3O2/c22-16-8-9-17(23)15(12-16)13-25-20(27)19-7-4-10-26(19)21(28)18(24)11-14-5-2-1-3-6-14/h1-3,5-6,8-9,12,18-19H,4,7,10-11,13,24H2,(H,25,27)/t18-,19+/m1/s1
InChIKeyXSOBNETYEYXSCD-MOPGFXCFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1ccc(cc1)CC(C(=O)N2CCCC2C(=O)NCc3cc(ccc3Cl)Cl)N
CACTVS 3.385N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3cc(Cl)ccc3Cl
ACDLabs 12.01O=C(NCc1cc(Cl)ccc1Cl)C3N(C(=O)C(N)Cc2ccccc2)CCC3
OpenEye OEToolkits 1.7.6c1ccc(cc1)C[C@H](C(=O)N2CCC[C@H]2C(=O)NCc3cc(ccc3Cl)Cl)N
CACTVS 3.385N[CH](Cc1ccccc1)C(=O)N2CCC[CH]2C(=O)NCc3cc(Cl)ccc3Cl
FormulaC21 H23 Cl2 N3 O2
NameD-phenylalanyl-N-(2,5-dichlorobenzyl)-L-prolinamide
ChEMBLCHEMBL2152433
DrugBank
ZINCZINC000095577194
PDB chain4udw Chain H Residue 1249 [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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PDB4udw Fragments Can Bind Either More Enthalpy or Entropy-Driven: Crystal Structures and Residual Hydration Pattern Suggest Why.
Resolution1.16 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D A190 S195 V213 S214 W215 G216 F227
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 A193 S198 V218 S219 W220 G221 F232
Annotation score1
Binding affinityMOAD: Kd=0.27uM
BindingDB: Kd=255nM
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:4udw, PDBe:4udw, PDBj:4udw
PDBsum4udw
PubMed26270568
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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