SMTL ID : 6y2i.1

Crystal structure of M. tuberculosis KasA in complex with N-(1H-indazol-5-yl)butane-1-sulfonamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

homo-dimer

Ligands

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 4 residues within 4Å: Chain A: V.403, V.404, A.405, R.409 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.403, A:A.405, A:R.409 EDO.2: 8 residues within 4Å: Chain A: R.140, E.143, S.144, L.147, V.156, S.157, A.160, M.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.143, A:S.157 EDO.3: 5 residues within 4Å: Chain A: S.230, R.233, A.234, M.235, T.237 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.233, A:M.235, A:M.235 Water bridges: A:S.230 EDO.4: 2 residues within 4Å: Chain A: R.98 Chain B: M.296 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.98, A:R.98, A:Q.162 EDO.5: 3 residues within 4Å: Chain A: D.325, A.354, Y.413 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.325 Water bridges: A:D.325, A:D.325 EDO.9: 5 residues within 4Å: Chain B: S.230, R.233, A.234, M.235, T.237 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.235, B:M.235 EDO.10: 5 residues within 4Å: Chain B: C.190, H.330, T.332, F.421, F.423 No protein-ligand interaction detected (PLIP) EDO.11: 6 residues within 4Å: Chain B: W.114, P.120, E.121, V.122, L.177, G.178 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.120, B:V.122 EDO.12: 4 residues within 4Å: Chain A: W.73, L.224 Chain B: Y.145, N.149 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.149, B:N.149 Water bridges: A:L.224 EDO.13: 6 residues within 4Å: Chain B: P.299, A.306, G.337, A.340, E.341, F.421 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.341 Water bridges: B:G.337

2 x O6Z: ~{N}-(1~{H}-indazol-5-yl)butane-1-sulfonamide(Non-covalent)

O6Z.6: 13 residues within 4Å: Chain A: G.136, E.139, E.218, G.219, P.220, I.221, E.222, P.225, F.229, F.258, H.364, I.366 Ligands: PG4.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.221, A:P.225, A:F.258 Hydrogen bonds: A:E.139, A:E.139, A:E.139, A:E.218, A:G.219 O6Z.14: 12 residues within 4Å: Chain B: G.136, E.139, E.218, G.219, P.220, I.221, E.222, P.225, F.258, H.364, I.366 Ligands: PG4.16 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:E.218, B:I.221, B:P.225, B:F.258, B:F.258 Hydrogen bonds: B:E.139, B:E.139, B:E.218, B:E.218, B:G.219 Water bridges: B:E.222

2 x NA: SODIUM ION(Non-functional Binders)

NA.7: 6 residues within 4Å: Chain A: N.328, A.329, H.330, E.373, N.418, N.419 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.419, A:N.419 NA.15: 6 residues within 4Å: Chain B: N.328, A.329, H.330, E.373, N.418, N.419 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.373, B:E.373, B:N.419

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.8: 10 residues within 4Å: Chain A: G.134, L.135, A.138, E.139, L.224, A.228, F.229 Chain B: I.164, M.165 Ligands: O6Z.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.134 PG4.16: 10 residues within 4Å: Chain A: V.161, I.164, M.165 Chain B: G.134, A.138, L.224, P.225, A.228, F.229 Ligands: O6Z.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cunningham, F. et al., Exploring the SAR of the beta-Ketoacyl-ACP Synthase Inhibitor GSK3011724A and Optimization around a Genotoxic Metabolite. Acs Infect Dis. (2020)

Release Date

2020-04-08

Peptides

3-oxoacyl-[acyl-carrier-protein] synthase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

3-oxoacyl-[acyl-carrier-protein] synthase 1

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