Structure of PDB 6l3x Chain C Binding Site BS01

Receptor Information
>6l3x Chain C (length=177) 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
TDRDNFLTAEEAKEYGLIDEVMVPETK
Ligand information
Ligand IDE4U
InChIInChI=1S/C23H26BCl2N3O4/c1-13(2)9-21(24(32)33)29-23(31)20(10-14-12-27-19-6-4-3-5-16(14)19)28-22(30)17-11-15(25)7-8-18(17)26/h3-8,11-13,20-21,27,32-33H,9-10H2,1-2H3,(H,28,30)(H,29,31)/t20-,21-/m0/s1
InChIKeyOIYFPOOZLADOLC-SFTDATJTSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7B(C(CC(C)C)NC(=O)C(Cc1c[nH]c2c1cccc2)NC(=O)c3cc(ccc3Cl)Cl)(O)O
OpenEye OEToolkits 2.0.7B([C@H](CC(C)C)NC(=O)[C@H](Cc1c[nH]c2c1cccc2)NC(=O)c3cc(ccc3Cl)Cl)(O)O
CACTVS 3.385CC(C)C[C@H](NC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)c3cc(Cl)ccc3Cl)B(O)O
CACTVS 3.385CC(C)C[CH](NC(=O)[CH](Cc1c[nH]c2ccccc12)NC(=O)c3cc(Cl)ccc3Cl)B(O)O
FormulaC23 H26 B Cl2 N3 O4
Name[(1~{R})-1-[[(2~{S})-2-[[2,5-bis(chloranyl)phenyl]carbonylamino]-3-(1~{H}-indol-3-yl)propanoyl]amino]-3-methyl-butyl]boronic acid
ChEMBLCHEMBL4446834
DrugBank
ZINC
PDB chain6l3x Chain C Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6l3x Discovery of Novel Peptidomimetic Boronate ClpP Inhibitors with Noncanonical Enzyme Mechanism as Potent Virulence Blockersin Vitroandin Vivo.
Resolution2.3054 Å
Binding residue
(original residue number in PDB)		G68 G69 S70 V71 S98 M99 H123 P125 L126 G127
Binding residue
(residue number reindexed from 1)		G50 G51 S52 V53 S80 M81 H105 P107 L108 G109
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:6l3x, PDBe:6l3x, PDBj:6l3x
PDBsum6l3x
PubMed32031798
UniProtQ2YSF8|CLPP_STAAB ATP-dependent Clp protease proteolytic subunit (Gene Name=clpP)

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