Structure of PDB 6l40 Chain D Binding Site BS01

Receptor Information
>6l40 Chain D (length=175) Species: 273036 (Staphylococcus aureus RF122) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPG
GSVTAGFAIYDTIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNA
EVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKD
TDRDNFLTAEEAKEYGLIDEVMVPE
Ligand information
Ligand IDFN3
InChIInChI=1S/C19H25BN4O4/c1-13(2)10-17(20(27)28)24-18(25)15(11-14-6-4-3-5-7-14)23-19(26)16-12-21-8-9-22-16/h3-9,12-13,15,17,27-28H,10-11H2,1-2H3,(H,23,26)(H,24,25)/t15-,17+/m0/s1
InChIKeyGXJABQQUPOEUTA-DOTOQJQBSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)C[CH](NC(=O)[CH](Cc1ccccc1)NC(=O)c2cnccn2)B(O)O
OpenEye OEToolkits 2.0.7B(C(CC(C)C)NC(=O)C(Cc1ccccc1)NC(=O)c2cnccn2)(O)O
OpenEye OEToolkits 2.0.7B([C@@H](CC(C)C)NC(=O)[C@H](Cc1ccccc1)NC(=O)c2cnccn2)(O)O
CACTVS 3.385CC(C)C[C@@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)c2cnccn2)B(O)O
FormulaC19 H25 B N4 O4
Name[(1S)-3-methyl-1-[[(2S)-3-phenyl-2-(pyrazin-2-ylcarbonylamino)propanoyl]amino]butyl]boronic acid
ChEMBLCHEMBL524664
DrugBank
ZINCZINC000169897614
PDB chain6l40 Chain D Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6l40 Discovery of Novel Peptidomimetic Boronate ClpP Inhibitors with Noncanonical Enzyme Mechanism as Potent Virulence Blockersin Vitroandin Vivo.
Resolution2.209 Å
Binding residue
(original residue number in PDB)		G69 V71 S98 H123 Q124 P125 L126
Binding residue
(residue number reindexed from 1)		G51 V53 S80 H105 Q106 P107 L108
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:6l40, PDBe:6l40, PDBj:6l40
PDBsum6l40
PubMed32031798
UniProtQ2YSF8|CLPP_STAAB ATP-dependent Clp protease proteolytic subunit (Gene Name=clpP)

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