SMTL ID : 5bs3.1

Crystal Structure of S.A. gyrase in complex with Compound 7

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: E.27, D.100 Chain C: 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.2: 5 residues within 4Å: Chain B: E.27, D.100, D.102 Chain D: 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.3, H2O.3

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

SO4.3: 3 residues within 4Å: Chain A: R.630 Chain B: R.630, R.633 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Salt bridges: A:R.630, B:R.630, B:R.633 Water bridges: B:D.628, B:R.633 SO4.4: 5 residues within 4Å: Chain C: G.5, T.6, A.7 Chain D: T.14, A.15 No protein-ligand interaction detected (PLIP) SO4.6: 5 residues within 4Å: Chain C: T.14, A.15 Chain D: G.5, T.6, A.7 No protein-ligand interaction detected (PLIP)

1 x WCP: (4R)-3-fluoro-4-hydroxy-4-{[(1r,4R)-4-{[(3-oxo-3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazin-6-yl)methyl]amino}-2-oxabicyclo[2.2.2]oct-1-yl]methyl}-4,5-dihydro-7H-pyrrolo[3,2,1-de][1,5]naphthyridin-7-one(Non-covalent)

WCP.5: 13 residues within 4Å: Chain A: A.269, G.273, M.276, D.284, M.322 Chain B: A.269, G.273, M.276, D.284 Chain C: G.10, C.11 Chain D: G.10, C.11 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:D.284, A:A.269 Hydrogen bonds: B:D.284

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, S.B. et al., Tricyclic 1,5-naphthyridinone oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad-spectrum antibacterial agents-SAR of left-hand-side moiety (Part-2). Bioorg.Med.Chem.Lett. (2015)

Release Date

2015-06-17

Peptides

DNA gyrase subunit A and B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

DNA gyrase subunit A and B

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