Structure of PDB 7dqu Chain A Binding Site BS02

Receptor Information

>7dqu Chain A (length=185) Species: 83333 (Escherichia coli K-12)

LDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHA
DNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLGVGVSVVNALSQKLELV
IQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFE
YEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHY

Ligand information

• Ligand ID: MPB
• InChI: InChI=1S/C8H8O3/c1-11-8(10)6-2-4-7(9)5-3-6/h2-5,9H,1H3
• InChIKey: LXCFILQKKLGQFO-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: COC(=O)c1ccc(cc1)O
  ACDLabs 10.04: O=C(OC)c1ccc(O)cc1
  CACTVS 3.341: COC(=O)c1ccc(O)cc1
• Formula: C8 H8 O3
• Name: 4-HYDROXY-BENZOIC ACID METHYL ESTER
• ChEMBL: CHEMBL325372
• DrugBank: DB14212
• ZINC: ZINC000000001712
• PDB chain: 7dqu Chain A Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7dqu Identification of new building blocks by fragment screening for discovering GyrB inhibitors.
• Resolution: 1.88 Å
• Binding residue (original residue number in PDB): V43 N46 A47 D73 I78 V120 T165
• Binding residue (residue number reindexed from 1): V28 N31 A32 D58 I63 V87 T132
• Annotation score: 1

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

External links

• PDB: RCSB:7dqu, PDBe:7dqu, PDBj:7dqu
• PDBsum: 7dqu
• PubMed: 34098257
• UniProt: P0AES6|GYRB_ECOLI DNA gyrase subunit B (Gene Name=gyrB)