Structure of PDB 7wid Chain I Binding Site BS01

Receptor Information
>7wid Chain I (length=191) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LIPTVIETTNRGERAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQ
AQDSEKDIYLYINSPGGSVTAGFAIYDTIQHIKPDVQTICIGMAASMGSF
LLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNR
ILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE
Ligand information
Ligand ID9DF
InChIInChI=1S/C27H33F3N4O3/c1-3-18(2)24-25(36)32(16-20-10-6-9-19-8-4-5-11-21(19)20)17-22-33(15-12-23(35)34(22)24)26(37)31-14-7-13-27(28,29)30/h4-6,8-11,18,22,24H,3,7,12-17H2,1-2H3,(H,31,37)/t18-,22+,24-/m0/s1
InChIKeyKQOUYKFBWWUWOZ-ANJVHQHFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCC(C)C1C(=O)N(CC2N1C(=O)CCN2C(=O)NCCCC(F)(F)F)Cc3cccc4c3cccc4
CACTVS 3.385CC[CH](C)[CH]1N2[CH](CN(Cc3cccc4ccccc34)C1=O)N(CCC2=O)C(=O)NCCCC(F)(F)F
OpenEye OEToolkits 2.0.7CC[C@H](C)[C@H]1C(=O)N(C[C@H]2N1C(=O)CCN2C(=O)NCCCC(F)(F)F)Cc3cccc4c3cccc4
CACTVS 3.385CC[C@H](C)[C@@H]1N2[C@H](CN(Cc3cccc4ccccc34)C1=O)N(CCC2=O)C(=O)NCCCC(F)(F)F
FormulaC27 H33 F3 N4 O3
Name(6S,9aS)-6-[(2S)-butan-2-yl]-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain7wid Chain I Residue 201 [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]
PDB7wid Anti-infective therapy using species-specific activators of Staphylococcus aureus ClpP.
Resolution1.9 Å
Binding residue
(original residue number in PDB)
L24 D27 I29 Y61 Y63 I91 I93
Binding residue
(residue number reindexed from 1)
L22 D25 I27 Y59 Y61 I89 I91
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

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:7wid, PDBe:7wid, PDBj:7wid
PDBsum7wid
PubMed36376309
UniProtQ2G036|CLPP_STAA8 ATP-dependent Clp protease proteolytic subunit (Gene Name=clpP)

[Back to BioLiP]