Structure of PDB 7dqf Chain A Binding Site BS02

Receptor Information
>7dqf Chain A (length=185) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHA
DNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLGVGVSVVNALSQKLELV
IQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFE
YEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHY
Ligand information
Ligand IDHF9
InChIInChI=1S/C8H8O4/c1-12-8(11)6-3-2-5(9)4-7(6)10/h2-4,9-10H,1H3
InChIKeyIIFCLXHRIYTHPV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7COC(=O)c1ccc(cc1O)O
CACTVS 3.385COC(=O)c1ccc(O)cc1O
FormulaC8 H8 O4
Namemethyl 2,4-bis(oxidanyl)benzoate
ChEMBLCHEMBL486026
DrugBank
ZINCZINC000000080786
PDB chain7dqf Chain A Residue 302 [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]
PDB7dqf Identification of new building blocks by fragment screening for discovering GyrB inhibitors.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		V43 N46 A47 D73 I78 V120 T165 V167
Binding residue
(residue number reindexed from 1)		V28 N31 A32 D58 I63 V87 T132 V134
Annotation score1
Enzymatic activity
Enzyme Commision number 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
GO:0005524 ATP binding
Biological Process
GO:0006265 DNA topological change

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:7dqf, PDBe:7dqf, PDBj:7dqf
PDBsum7dqf
PubMed34098257
UniProtP0AES6|GYRB_ECOLI DNA gyrase subunit B (Gene Name=gyrB)

[Back to BioLiP]