SMTL ID : 7lhz.1 (1 other biounit)

K. pneumoniae Topoisomerase IV (ParE-ParC) in complex with DNA and (3S)-10-[(3R)-3-(1-aminocyclopropyl)pyrrolidin-1-yl]-9-fluoro-3-methyl-5-oxo-2,3-dihydro-5H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid (compound 25)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-dimer

Ligands

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 8 residues within 4Å: Chain A: R.617, I.620, L.624, A.661, E.664, L.665, H.669, I.678 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.617, A:R.617

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.103, D.105, K.177, G.178 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.103, A:D.103, A:D.105, A:D.105 MG.3: 2 residues within 4Å: Chain B: D.103, D.105 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.103, B:D.105, B:D.105

2 x Y21: (3S)-10-[(3R)-3-(1-aminocyclopropyl)pyrrolidin-1-yl]-9-fluoro-3-methyl-5-oxo-2,3-dihydro-5H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid(Non-covalent)

Y21.4: 12 residues within 4Å: Chain A: K.54, G.55, E.73, G.323, D.324, S.325, A.326 Chain B: R.364 Chain C: C.4, A.5 Chain E: G.1 Chain F: T.11 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.54 Hydrogen bonds: A:K.54, A:E.73, A:D.324, A:S.325, A:A.326 Salt bridges: B:R.364 Y21.5: 11 residues within 4Å: Chain B: K.54, G.55, E.73, G.323, D.324, S.325, A.326 Chain C: G.1 Chain D: T.11 Chain E: C.4, A.5 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:K.54, B:E.73 Hydrogen bonds: B:K.54, B:D.324, B:S.325, B:A.326

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lapointe, G. et al., Discovery and Optimization of DNA Gyrase and Topoisomerase IV Inhibitors with Potent Activity against Fluoroquinolone-Resistant Gram-Positive Bacteria. J.Med.Chem. (2021)

Release Date

2021-05-12

Peptides

DNA topoisomerase 4 subunit B, DNA topoisomerase 4 subunit A chimera: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA topoisomerase 4 subunit B, DNA topoisomerase 4 subunit A chimera

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