Structure of PDB 8ylb Chain B Binding Site BS02

Receptor Information
>8ylb Chain B (length=173) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LIPIVVAYDIYSRLLRERIVCVMGPIDDSVASLVIAQLLFLQSESNKKPI
HMYINSPGGVVTAGLAIYDTMQYILNPICTWCVGQAASMGSLLLAAGTPG
MRHSLPNSRIMIHQPSAIQAEEIMKLKKQLYNIYAKHTKQSLQVIESAME
RDRYMSPMEAQEFGILDKVLVHP
Ligand information
Ligand IDA1LZA
InChIInChI=1S/C24H26N4O/c1-18-7-5-6-10-20(18)16-27-13-14-28-22-11-12-26(15-19-8-3-2-4-9-19)17-21(22)23(29)25-24(27)28/h2-10H,11-17H2,1H3
InChIKeyCPQVAKZHOMXNHY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ccccc1CN2CCN3C4=C(CN(CC4)Cc5ccccc5)C(=O)N=C23
OpenEye OEToolkits 2.0.7Cc1ccccc1CN2CCN3C2=NC(=O)C4=C3CCN(C4)Cc5ccccc5
FormulaC24 H26 N4 O
Name5-[(2-methylphenyl)methyl]-11-(phenylmethyl)-2,5,7,11-tetrazatricyclo[7.4.0.0^{2,6}]trideca-1(9),6-dien-8-one
ChEMBL
DrugBank
ZINC
PDB chain8ylb Chain C 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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PDB8ylb Rational Design of a Novel Class of Human ClpP Agonists through a Ring-Opening Strategy with Enhanced Antileukemia Activity.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		L104 S108 Y138
Binding residue
(residue number reindexed from 1)		L39 S43 Y73
Annotation score1
Enzymatic activity
Enzyme Commision number 3.4.21.92: endopeptidase Clp.
Gene Ontology
Molecular Function
GO:0004176 ATP-dependent peptidase activity
GO:0004252 serine-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

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Molecular Function
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Biological Process
External links
PDB RCSB:8ylb, PDBe:8ylb, PDBj:8ylb
PDBsum8ylb
PubMed38620134
UniProtQ16740|CLPP_HUMAN ATP-dependent Clp protease proteolytic subunit, mitochondrial (Gene Name=CLPP)

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