Structure of PDB 5lce Chain H Binding Site BS03

Receptor Information
>5lce 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 ID6TH
InChIInChI=1S/C22H32ClN3O3/c23-18-9-8-16(14-27)17(12-18)13-25-21(28)20-7-4-10-26(20)22(29)19(24)11-15-5-2-1-3-6-15/h8-9,12,15,19-20,27H,1-7,10-11,13-14,24H2,(H,25,28)/t19-,20+/m1/s1
InChIKeyDQPDUJDTFYTAKL-UXHICEINSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.5c1cc(c(cc1Cl)CNC(=O)[C@@H]2CCCN2C(=O)[C@@H](CC3CCCCC3)N)CO
CACTVS 3.385N[CH](CC1CCCCC1)C(=O)N2CCC[CH]2C(=O)NCc3cc(Cl)ccc3CO
CACTVS 3.385N[C@H](CC1CCCCC1)C(=O)N2CCC[C@H]2C(=O)NCc3cc(Cl)ccc3CO
OpenEye OEToolkits 2.0.5c1cc(c(cc1Cl)CNC(=O)C2CCCN2C(=O)C(CC3CCCCC3)N)CO
FormulaC22 H32 Cl N3 O3
Name(2~{S})-1-[(2~{R})-2-azanyl-3-cyclohexyl-propanoyl]-~{N}-[[5-chloranyl-2-(hydroxymethyl)phenyl]methyl]pyrrolidine-2-carboxamide
ChEMBLCHEMBL4459217
DrugBank
ZINC
PDB chain5lce Chain H Residue 301 [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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PDB5lce Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding.
Resolution1.39 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D N98 A190 S195 V213 S214 W215 G216 F227
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 N95 A193 S198 V218 S219 W220 G221 F232
Annotation score1
Binding affinityBindingDB: Ki=9.2nM
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:5lce, PDBe:5lce, PDBj:5lce
PDBsum5lce
PubMed31633354
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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