Structure of PDB 8qyf Chain B Binding Site BS01

Receptor Information
>8qyf Chain B (length=178) Species: 1282 (Staphylococcus epidermidis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IPTYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYI
NSPGGSVTAGFAIYDTIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFA
LPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEK
IQQDTDRDNFLTAAEAKEYGLIDEVMEP
Ligand information
Ligand ID6V8
InChIInChI=1S/C14H19BCl2N2O4/c1-8(2)5-12(15(22)23)19-13(20)7-18-14(21)10-6-9(16)3-4-11(10)17/h3-4,6,8,12,22-23H,5,7H2,1-2H3,(H,18,21)(H,19,20)/t12-/m0/s1
InChIKeyMXAYKZJJDUDWDS-LBPRGKRZSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)C[C@H](NC(=O)CNC(=O)c1cc(Cl)ccc1Cl)B(O)O
OpenEye OEToolkits 2.0.5B(C(CC(C)C)NC(=O)CNC(=O)c1cc(ccc1Cl)Cl)(O)O
OpenEye OEToolkits 2.0.5B([C@H](CC(C)C)NC(=O)CNC(=O)c1cc(ccc1Cl)Cl)(O)O
CACTVS 3.385CC(C)C[CH](NC(=O)CNC(=O)c1cc(Cl)ccc1Cl)B(O)O
FormulaC14 H19 B Cl2 N2 O4
Name[(1~{R})-1-[2-[[2,5-bis(chloranyl)phenyl]carbonylamino]ethanoylamino]-3-methyl-butyl]boronic acid
ChEMBLCHEMBL2141296
DrugBankDB09570
ZINCZINC000169946773
PDB chain8qyf Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8qyf Molecular insights into the dynamic modulation of bacterial ClpP function and oligomerization by peptidomimetic boronate compounds
Resolution2.33 Å
Binding residue
(original residue number in PDB)		G68 G69 V71 S98 M99 H123 Q124 P125 L126 H142 I143 T146
Binding residue
(residue number reindexed from 1)		G54 G55 V57 S84 M85 H109 Q110 P111 L112 H128 I129 T132
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
GO:0008236 serine-type peptidase activity
GO:0051117 ATPase binding
Biological Process
GO:0006508 proteolysis
GO:0006515 protein quality control for misfolded or incompletely synthesized proteins
Cellular Component
GO:0005737 cytoplasm
GO:0009368 endopeptidase Clp complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8qyf, PDBe:8qyf, PDBj:8qyf
PDBsum8qyf
PubMed38296985
UniProtQ5HQW0|CLPP_STAEQ ATP-dependent Clp protease proteolytic subunit (Gene Name=clpP)

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