SMTL ID : 6p9l.1

Crystal structure of Mycobacterium tuberculosis KasA in complex with JFX

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-dimer

Ligands

2 x JFX: 4-fluoro-N-(3-methyl-1H-indazol-5-yl)butane-1-sulfonamide(Non-covalent)

JFX.1: 15 residues within 4Å: Chain A: L.114, G.115, E.118, E.197, G.198, P.199, I.200, E.201, P.204, F.237, G.238, E.239, H.343, I.345 Ligands: IPA.6 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.114, A:E.197, A:E.201, A:F.237 Hydrogen bonds: A:E.118, A:E.118, A:E.118, A:E.197, A:G.198 Water bridges: A:Y.80 JFX.9: 15 residues within 4Å: Chain B: L.114, G.115, E.118, E.197, G.198, P.199, I.200, E.201, P.204, F.237, G.238, E.239, H.343, I.345 Ligands: IPA.14 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.114, B:E.197, B:E.201, B:F.237 Hydrogen bonds: B:E.118, B:E.118, B:E.197, B:E.197, B:G.198 Water bridges: B:Y.80

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

NA.2: 6 residues within 4Å: Chain A: N.307, A.308, H.309, E.352, N.397, N.398 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.307, A:N.398 NA.10: 6 residues within 4Å: Chain B: N.307, A.308, H.309, E.352, N.397, N.398 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.352, B:N.398

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: A.16, V.17, I.27, E.28, S.95, R.361 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.17, A:E.28, A:S.95, A:R.361 GOL.11: 6 residues within 4Å: Chain B: A.16, V.17, I.27, E.28, S.95, R.361 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.17, B:E.28, B:E.28, B:S.95, B:R.361

10 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.4: 3 residues within 4Å: Chain A: A.280, D.281, N.322 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.280, A:D.281 Hydrogen bonds: A:N.322 IPA.5: 3 residues within 4Å: Chain A: F.273, A.280, D.281 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.273, A:D.281 Hydrogen bonds: A:A.280 IPA.6: 3 residues within 4Å: Chain A: G.113 Chain B: M.144 Ligands: JFX.1 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:M.144 IPA.7: 6 residues within 4Å: Chain A: M.211, A.213, V.276, T.313, I.315, F.402 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.213, A:T.313, A:I.315, A:F.402 Hydrogen bonds: A:M.211 IPA.8: 4 residues within 4Å: Chain A: D.281, N.322, R.325, V.326 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.322, A:R.325 Hydrogen bonds: A:N.322, A:R.325 IPA.12: 3 residues within 4Å: Chain B: A.280, D.281, N.322 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.280, B:D.281 Hydrogen bonds: B:N.322 IPA.13: 3 residues within 4Å: Chain B: F.273, A.280, D.281 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.273, B:D.281 Hydrogen bonds: B:A.280 IPA.14: 3 residues within 4Å: Chain A: M.144 Chain B: G.113 Ligands: JFX.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:M.144 IPA.15: 6 residues within 4Å: Chain B: M.211, A.213, V.276, T.313, I.315, F.402 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.213, B:T.313, B:I.315, B:F.402 Hydrogen bonds: B:M.211 IPA.16: 4 residues within 4Å: Chain B: D.281, N.322, R.325, V.326 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:N.322, B:R.325 Hydrogen bonds: B:N.322, B:R.325

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Inoyama, D. et al., A Preclinical Candidate Targeting Mycobacterium tuberculosis KasA. Cell Chem Biol (2020)

Release Date

2020-04-01

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

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

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