SMTL ID : 7fvt.1

Crystal Structure of S. aureus gyrase in complex with 6-[5-[2-[(4-chloro-2,3-dihydro-1H-inden-2-yl)methylamino]ethyl]-2-oxo-1,3-oxazolidin-3-yl]-4H-pyrido[3,2-b][1,4]oxazin-3-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-dimer

Ligands

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: E.27, D.100, D.102 Chain D: G.8, G.9 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.27, A:D.100, H2O.1, H2O.2 MN.3: 4 residues within 4Å: Chain B: E.27, D.100 Chain C: G.8, G.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.27, B:D.100, H2O.10, H2O.13 MN.4: 4 residues within 4Å: Chain B: Y.523, K.524, T.526, Q.529 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:Y.523, B:T.526, B:Q.529, H2O.17, H2O.17

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: R.630 Chain B: R.630 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain B: D.339, I.340, N.341, K.342 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain B: N.470, R.473 Ligand excluded by PLIP

1 x 6I0: 6-{(5R)-5-[2-({[(2R)-4-chloro-2,3-dihydro-1H-inden-2-yl]methyl}amino)ethyl]-2-oxo-1,3-oxazolidin-3-yl}-2H-pyrido[3,2-b][1,4]oxazin-3(4H)-one(Non-covalent)

6I0.7: 15 residues within 4Å: Chain A: A.269, V.272, G.273, M.276, D.284 Chain B: A.269, G.273, D.284, A.321, M.322, R.323 Chain C: G.10, C.11 Chain D: G.10, C.11 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:D.284, B:A.269 Hydrogen bonds: B:D.284, B:R.323, B:R.323

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cumming, J.G. et al., Discovery of a Series of Indane-Containing NBTIs with Activity against Multidrug-Resistant Gram-Negative Pathogens. Acs Med.Chem.Lett. (2023)

Release Date

2023-06-28

Peptides

DNA gyrase subunit B,DNA gyrase subunit A Chimera: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA gyrase subunit B,DNA gyrase subunit A Chimera

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