SMTL ID : 5iwi.1

1.98A structure of GSK945237 with S.aureus DNA gyrase and singly nicked DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

hetero-2-2-mer

Ligands

1 x DT- DG- DT- DG- DC- DG- DG- DT: DNA (5'-D(*TP*GP*TP*GP*CP*GP*GP*T*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')(Non-covalent)

DT-DG-DT-DG-DC-DG-DG-DT.1: 30 residues within 4Å: Chain B: R.121 Chain C: E.27, G.51, K.52, D.104, I.108 Chain D: R.32, K.42, V.44, H.45, H.78, H.80, G.81, S.84, R.91, S.172, I.174, Q.266, R.271 Chain E: A.13, C.14, C.15, G.16, C.17, A.18, C.19, A.20 Chain F: G.1, T.12 Ligands: GOL.15 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 2 interactions with chain D Hydrogen bonds: C:S.30, B:R.121 Salt bridges: C:R.50 Water bridges: D:S.83, D:S.83

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

MN.2: 4 residues within 4Å: Chain A: E.27, D.100 Chain E: 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.1 MN.10: 3 residues within 4Å: Chain C: D.100, D.102, K.139 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.102, H2O.17, H2O.18, H2O.19 MN.11: 1 residues within 4Å: Chain D: H.389 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.389, H2O.23, H2O.31

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain B: F.96, S.111, M.112, G.114, Q.266 Chain E: C.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:M.112, B:G.114 Water bridges: B:Q.94, B:S.111, B:D.115 GOL.4: 6 residues within 4Å: Chain B: A.31, P.43, R.46, R.47, E.155, P.156 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.46, B:P.156 Water bridges: B:R.47 GOL.5: 5 residues within 4Å: Chain B: D.95, F.96, M.112, P.218, R.484 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.484 GOL.6: 4 residues within 4Å: Chain B: E.249, V.259, T.261, R.302 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.302, B:R.302 Water bridges: B:E.249, B:R.257 GOL.7: 3 residues within 4Å: Chain B: N.53, E.54, N.139 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.53, B:N.139 GOL.8: 2 residues within 4Å: Chain B: N.312, V.315 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.312 Water bridges: B:S.314 GOL.12: 6 residues within 4Å: Chain D: P.43, R.46, R.47, I.146, E.155, P.156 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:P.43, D:R.46 GOL.13: 4 residues within 4Å: Chain D: E.250, G.254, R.255, Q.256 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.254, D:G.254 Water bridges: D:Q.256 GOL.14: 4 residues within 4Å: Chain D: E.381, R.384, I.385, Y.444 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.384, D:R.384 GOL.15: 6 residues within 4Å: Chain D: F.96, M.112, Q.266, V.267, N.268 Ligands: DT-DG-DT-DG-DC-DG-DG-DT.1 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.266, D:V.267

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

CL.9: 2 residues within 4Å: Chain B: N.312, S.314 Ligand excluded by PLIP

1 x 6EJ: (1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one(Non-covalent)

6EJ.16: 13 residues within 4Å: Chain B: A.67, G.71, M.74, D.82, M.120 Chain D: A.67, G.71, M.74, D.82 Chain E: T.10, A.11 Chain F: T.2, A.3 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:D.82 Water bridges: B:R.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miles, T.J. et al., Novel tricyclics (e.g., GSK945237) as potent inhibitors of bacterial type IIA topoisomerases. Bioorg.Med.Chem.Lett. (2016)

Release Date

2016-05-25

Peptides

DNA gyrase subunit B,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 B

DNA gyrase subunit A

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