Structure of PDB 5boc Chain A Binding Site BS01

Receptor Information

>5boc Chain A (length=192) Species: 171101 (Streptococcus pneumoniae R6)

QVLEGLDAVRKRPGMYIGSTDGAGLHHLVWEIVDNAVDEALSGFGDRIDV
TINKDGSLTVQDHGRGMPTGMHAMGIPTVEVIFTILHVGSSVVNALSSWL
EVEITRDGAVYKQRFENGGKPVTTLKKIGTALKSKTGTKVTFMPDATIFS
TTDFKYNTISERLNESAFLLKNVTLSLTDKRTDEAIEFHYEN

Ligand information

• Ligand ID: TSJ
• InChI: InChI=1S/C20H16F3N3O3/c1-10-5-13(8-14(6-10)20(21,22)23)16-9-17(26-25-16)24-18(27)15-4-3-12(19(28)29)7-11(15)2/h3-9H,1-2H3,(H,28,29)(H2,24,25,26,27)
• InChIKey: MLGFDWKUOYDRDY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: FC(F)(F)c1cc(cc(c1)C)c2cc(nn2)NC(=O)c3c(cc(cc3)C(=O)O)C
  OpenEye OEToolkits 1.9.2: Cc1cc(cc(c1)C(F)(F)F)c2cc([nH]n2)NC(=O)c3ccc(cc3C)C(=O)O
  CACTVS 3.385: Cc1cc(cc(c1)C(F)(F)F)c2cc([nH]n2)NC(=O)c3ccc(cc3C)C(O)=O
• Formula: C20 H16 F3 N3 O3
• Name: 3-methyl-4-({3-[3-methyl-5-(trifluoromethyl)phenyl]-1H-pyrazol-5-yl}carbamoyl)benzoic acid
• ChEMBL: CHEMBL3986668
• ZINC: ZINC000230586492
• PDB chain: 5boc Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5boc Application of Fragment-based Drug Discovery against DNA GyraseB
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): N51 E55 D78 R81 M83 F99 S124 T172
• Binding residue (residue number reindexed from 1): N35 E39 D62 R65 M67 F83 S90 T138
• 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:5boc, PDBe:5boc, PDBj:5boc
• PDBsum: 5boc
• UniProt: Q8DQB5