SMTL ID : 7fvs.1

Crystal Structure of S. aureus gyrase in complex with 4-[[1-[(1-chloro-6,7-dihydro-5H-cyclopenta[c]pyridin-6-yl)methyl]azetidin-3-yl]methylamino]-6-fluorochromen-2-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 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 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.27, A:E.27, A:D.100, H2O.1, H2O.1 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.8, 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.13, H2O.13

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

CL.2: 1 residues within 4Å: Chain A: R.630 Ligand excluded by PLIP

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 4 residues within 4Å: Chain B: D.339, I.340, N.341, K.342 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:N.341 Hydrogen bonds: B:D.339, B:I.340, B:N.341 Salt bridges: B:K.342

1 x 61I: 4-{[(1-{[(6R)-1-chloro-6,7-dihydro-5H-cyclopenta[c]pyridin-6-yl]methyl}azetidin-3-yl)methyl]amino}-6-fluoro-2H-1-benzopyran-2-one(Non-covalent)

61I.6: 13 residues within 4Å: Chain A: A.269, M.276, D.284, M.322, R.323 Chain B: A.269, G.273, M.276, D.284 Chain C: G.10, C.11 Chain D: G.10, C.11 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:A.269, B:D.284 Water bridges: A:R.323 Salt bridges: A:D.284, B:D.284 Hydrogen bonds: B:D.284, B:D.284

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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