SMTL ID : 7mvs.1

DNA gyrase complexed with uncleaved DNA and Compound 7 to 2.6A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: P.246, R.249, I.349, S.360 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: R.631 Chain B: R.631 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain B: R.189, M.381, P.545 Ligand excluded by PLIP

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

MN.2: 5 residues within 4Å: Chain A: E.28, D.101 Chain B: F.325 Chain C: G.8, G.9 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.28, A:D.101, H2O.1 MN.6: 4 residues within 4Å: Chain B: E.28, D.101 Chain D: G.8, G.9 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.28, B:D.101

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

SO4.5: 6 residues within 4Å: Chain B: P.246, R.249, R.250, I.349, E.358, S.360 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.358 Water bridges: B:E.358 Salt bridges: B:R.249, B:R.250

1 x Y1W: (1S)-2-[(2r,5S)-5-{[(2,3-dihydro-1,4-benzodioxin-6-yl)methyl]amino}-1,3-dioxan-2-yl]-1-(3-fluoro-6-methoxyquinolin-4-yl)ethan-1-ol(Non-covalent)

Y1W.7: 17 residues within 4Å: Chain A: A.270, V.273, G.274, M.277, D.285, M.323 Chain B: A.270, V.273, G.274, M.277, D.285, M.323, R.324 Chain C: G.10, C.11 Chain D: G.10, C.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.285 Hydrogen bonds: A:D.285

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, Y. et al., Optimization of TopoIV Potency, ADMET Properties, and hERG Inhibition of 5-Amino-1,3-dioxane-Linked Novel Bacterial Topoisomerase Inhibitors: Identification of a Lead with In Vivo Efficacy against MRSA. J.Med.Chem. (2021)

Release Date

2021-10-20

Peptides

DNA gyrase subunit B,DNA gyrase subunit A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA gyrase subunit B,DNA gyrase subunit A