Structure of PDB 5lpd Chain H Binding Site BS02

Receptor Information
>5lpd 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
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWGQ
PSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSG
GPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQ
F
Ligand information
Ligand ID71U
InChIInChI=1S/C22H33ClN4O2/c23-18-9-8-16(13-24)17(12-18)14-26-21(28)20-7-4-10-27(20)22(29)19(25)11-15-5-2-1-3-6-15/h8-9,12,15,19-20H,1-7,10-11,13-14,24-25H2,(H,26,28)/t19-,20+/m1/s1
InChIKeyKFAWBGCOGBILHI-UXHICEINSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.5c1cc(c(cc1Cl)CNC(=O)C2CCCN2C(=O)C(CC3CCCCC3)N)CN
CACTVS 3.385NCc1ccc(Cl)cc1CNC(=O)[C@@H]2CCCN2C(=O)[C@H](N)CC3CCCCC3
OpenEye OEToolkits 2.0.5c1cc(c(cc1Cl)CNC(=O)[C@@H]2CCCN2C(=O)[C@@H](CC3CCCCC3)N)CN
CACTVS 3.385NCc1ccc(Cl)cc1CNC(=O)[CH]2CCCN2C(=O)[CH](N)CC3CCCCC3
FormulaC22 H33 Cl N4 O2
Name(2~{S})-~{N}-[[2-(aminomethyl)-5-chloranyl-phenyl]methyl]-1-[(2~{R})-2-azanyl-3-cyclohexyl-propanoyl]pyrrolidine-2-carboxamide
ChEMBLCHEMBL4457051
DrugBank
ZINC
PDB chain5lpd Chain H Residue 307 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5lpd Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D N98 A190 E192 S195 V213 S214 W215 G216 G219 F227
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 N95 A194 E196 S199 V219 S220 W221 G222 G224 F233
Annotation score1
Binding affinityBindingDB: Ki=0.070000nM
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:5lpd, PDBe:5lpd, PDBj:5lpd
PDBsum5lpd
PubMed31633354
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

[Back to BioLiP]