SMTL ID : 6qx1.1

2.7A structure of benzoisoxazole 3 with S.aureus DNA gyrase and DNA.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

hetero-2-2-mer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: E.27, D.100, D.102 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.100, A:D.102, H2O.1, H2O.1, H2O.1, H2O.12 MN.5: 3 residues within 4Å: Chain C: E.27, D.100, D.102 6 PLIP interactions: 2 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.100, C:D.102, H2O.6, H2O.6, H2O.6, H2O.13

2 x JK8: (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine(Non-covalent)

JK8.2: 10 residues within 4Å: Chain A: R.188, I.191, E.192, A.195 Chain B: M.26, I.29, V.30, M.178, R.341, P.342 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.191, A:E.192, A:A.195, B:P.342, B:P.342 Hydrogen bonds: A:R.188, B:P.342 JK8.6: 11 residues within 4Å: Chain C: R.188, I.191, E.192, A.195 Chain D: M.26, I.29, V.30, M.178, I.335, R.341, P.342 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:I.191, C:E.192, C:A.195, D:I.335, D:P.342 Hydrogen bonds: C:R.188, D:P.342

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain B: N.312, S.314, V.315 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.312 GOL.4: 6 residues within 4Å: Chain B: P.43, R.46, R.47, E.155, P.156, S.157 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.43, B:R.46, B:S.157 GOL.9: 8 residues within 4Å: Chain D: F.96, S.111, M.112, G.114, Q.266, V.267, N.268 Chain F: C.4 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.266, D:V.267 Water bridges: D:V.267 GOL.10: 5 residues within 4Å: Chain B: S.83 Chain E: A.7, G.8, G.9, T.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.83 Water bridges: B:S.84, B:S.84 GOL.11: 3 residues within 4Å: Chain E: G.17, G.18 Chain F: G.2 No protein-ligand interaction detected (PLIP)

1 x GLY: GLYCINE(Covalent)

GLY.7: 3 residues within 4Å: Chain D: G.225, Q.488, L.489 No protein-ligand interaction detected (PLIP)

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

CL.8: 2 residues within 4Å: Chain D: N.312, S.314 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thalji, R.K. et al., Structure-guided design of antibacterials that allosterically inhibit DNA gyrase. Bioorg.Med.Chem.Lett. (2019)

Release Date

2019-04-17

Peptides

DNA gyrase subunit B: AC
DNA gyrase subunit A: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
D

B
A

D
C

DNA gyrase subunit B

DNA gyrase subunit A

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