SMTL ID : 7pqi.1

Acinetobacter baumannii DNA gyrase B 23kDa ATPase subdomain complexed with novobiocin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x NOV: NOVOBIOCIN(Non-covalent)

NOV.1: 17 residues within 4Å: Chain A: N.33, A.34, D.36, E.37, D.60, R.63, G.64, I.65, P.66, D.68, H.70, A.77, I.81, V.107, R.123, T.152 Ligands: EDO.6 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:P.66, A:I.81, A:I.81 Hydrogen bonds: A:N.33, A:D.60, A:H.70 Water bridges: A:N.33, A:D.36, A:D.60, A:D.60, A:G.62, A:R.63, A:R.63, A:T.152 Salt bridges: A:R.63, A:R.123 pi-Cation interactions: A:R.63, A:R.63

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: E.45, I.47, S.59, D.60, N.61 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.45 EDO.3: 5 residues within 4Å: Chain A: E.171, A.174, R.175, R.178, H.200 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.175, A:R.178, A:R.178 EDO.4: 4 residues within 4Å: Chain A: R.9, P.10, G.11, M.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.9, A:G.11, A:M.12 EDO.5: 9 residues within 4Å: Chain A: S.59, D.60, Y.122, N.149, T.150, G.151, T.152, T.153 Ligands: EDO.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.60, A:T.152 EDO.6: 5 residues within 4Å: Chain A: P.66, T.67, D.68, R.123 Ligands: NOV.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.67, A:T.67, A:D.68, A:R.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cotman, A.E. et al., Discovery and Hit-to-Lead Optimization of Benzothiazole Scaffold-Based DNA Gyrase Inhibitors with Potent Activity against Acinetobacter baumannii and Pseudomonas aeruginosa. J.Med.Chem. (2023)

Release Date

2022-09-28

Peptides

DNA gyrase subunit B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA gyrase subunit B

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