SMTL ID : 6m1j.1 (1 other biounit)

The DNA Gyrase B ATP binding domain of PSEUDOMONAS AERUGINOSA in complex with compound 12x

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 4 residues within 4Å: Chain A: R.118, V.131, F.139, R.142 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.118, A:R.118 Water bridges: A:R.142 Salt bridges: A:E.129

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: S.169, D.171, I.172 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.169, A:S.169, A:D.171 Water bridges: A:D.171 SO4.3: 5 residues within 4Å: Chain A: P.66, V.67, D.68, R.123, H.124 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.67, A:D.68 Water bridges: A:H.124, A:H.124 Salt bridges: A:R.123, A:H.124

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain A: N.61, G.62, S.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.150, A:S.150 Water bridges: A:S.150

1 x EZ6: 1-[5-[6-fluoranyl-8-(methylamino)-4-[3-(trifluoromethyl)pyrazol-1-yl]-9H-pyrido[2,3-b]indol-3-yl]pyrimidin-2-yl]cyclopropane-1-carboxylic acid(Non-covalent)

EZ6.5: 13 residues within 4Å: Chain A: V.30, N.33, S.34, E.37, V.58, D.60, R.63, G.64, I.65, P.66, I.81, V.107, T.152 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:N.33, A:I.65, A:I.65 Hydrogen bonds: A:D.60, A:D.60, A:R.63, A:T.152 Water bridges: A:G.64 Salt bridges: A:R.63 pi-Cation interactions: A:R.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, Y. et al., Discovery of Pyrido[2,3-b]indole Derivatives with Gram-Negative Activity Targeting Both DNA Gyrase and Topoisomerase IV. J.Med.Chem. (2020)

Release Date

2020-09-02

Peptides

DNA gyrase subunit B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA gyrase subunit B

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