SMTL ID : 8f4t.1

Crystal structure of acetyltransferase Eis from M. tuberculosis in complex with proguanil

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-hexamer

Ligands

6 x XEW: N-(4-chlorophenyl)-N'-(propan-2-yl)triimidodicarbonic diamide(Non-covalent)

XEW.1: 12 residues within 4Å: Chain A: W.33, D.46, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.56, A:V.60, A:L.83, A:F.104 Hydrogen bonds: A:S.103, A:F.422, A:F.422 Water bridges: A:F.104 Salt bridges: A:D.46 pi-Cation interactions: A:W.56, A:W.56, A:W.56 XEW.8: 12 residues within 4Å: Chain B: W.33, D.46, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.56, B:V.60, B:L.83, B:F.104 Hydrogen bonds: B:S.103, B:F.422, B:F.422 Water bridges: B:F.104 Salt bridges: B:D.46 pi-Cation interactions: B:W.56, B:W.56, B:W.56 XEW.15: 12 residues within 4Å: Chain C: W.33, D.46, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:W.56, C:V.60, C:L.83, C:F.104 Hydrogen bonds: C:S.103, C:F.422, C:F.422 Water bridges: C:F.104 Salt bridges: C:D.46 pi-Cation interactions: C:W.56, C:W.56, C:W.56 XEW.22: 12 residues within 4Å: Chain D: W.33, D.46, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:W.56, D:V.60, D:L.83, D:F.104 Hydrogen bonds: D:S.103, D:F.422, D:F.422, D:F.422 Water bridges: D:F.104 Salt bridges: D:D.46 pi-Cation interactions: D:W.56, D:W.56, D:W.56 XEW.29: 12 residues within 4Å: Chain E: W.33, D.46, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:W.56, E:V.60, E:L.83, E:F.104 Hydrogen bonds: E:S.103, E:F.422, E:F.422, E:F.422 Water bridges: E:F.104 Salt bridges: E:D.46 pi-Cation interactions: E:W.56, E:W.56, E:W.56 XEW.36: 12 residues within 4Å: Chain F: W.33, D.46, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:W.56, F:V.60, F:L.83, F:F.104 Hydrogen bonds: F:S.103, F:F.422, F:F.422, F:F.422 Water bridges: F:F.104 Salt bridges: F:D.46 pi-Cation interactions: F:W.56, F:W.56, F:W.56

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: F.44, S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligand excluded by PLIP GOL.3: 6 residues within 4Å: Chain A: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.4: 8 residues within 4Å: Chain A: L.157, R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.5 Ligand excluded by PLIP GOL.7: 7 residues within 4Å: Chain A: P.28, W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP GOL.9: 8 residues within 4Å: Chain B: F.44, S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligand excluded by PLIP GOL.10: 6 residues within 4Å: Chain B: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.11: 8 residues within 4Å: Chain B: L.157, R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.12 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain B: P.28, W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP GOL.16: 8 residues within 4Å: Chain C: F.44, S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain C: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.18: 8 residues within 4Å: Chain C: L.157, R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.19 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain C: P.28, W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP GOL.23: 8 residues within 4Å: Chain D: F.44, S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligand excluded by PLIP GOL.24: 6 residues within 4Å: Chain D: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.25: 8 residues within 4Å: Chain D: L.157, R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.26 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain D: P.28, W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP GOL.30: 8 residues within 4Å: Chain E: F.44, S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain E: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.32: 8 residues within 4Å: Chain E: L.157, R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.33 Ligand excluded by PLIP GOL.35: 7 residues within 4Å: Chain E: P.28, W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP GOL.37: 8 residues within 4Å: Chain F: F.44, S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligand excluded by PLIP GOL.38: 6 residues within 4Å: Chain F: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.39: 8 residues within 4Å: Chain F: L.157, R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.40 Ligand excluded by PLIP GOL.42: 7 residues within 4Å: Chain F: P.28, W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 9 residues within 4Å: Chain A: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.289 Water bridges: A:L.261, A:L.261 PEG.12: 9 residues within 4Å: Chain B: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 Ligands: GOL.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.289 Water bridges: B:L.261, B:L.261 PEG.19: 9 residues within 4Å: Chain C: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 Ligands: GOL.18 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.289 Water bridges: C:L.261, C:L.261 PEG.26: 9 residues within 4Å: Chain D: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 Ligands: GOL.25 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.293 Water bridges: D:L.261, D:L.261 PEG.33: 9 residues within 4Å: Chain E: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 Ligands: GOL.32 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.293 Water bridges: E:L.261, E:L.261 PEG.40: 9 residues within 4Å: Chain F: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 Ligands: GOL.39 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:D.293 Water bridges: F:L.261, F:L.261

6 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.6: 8 residues within 4Å: Chain A: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, D.413 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.413 DMS.13: 8 residues within 4Å: Chain B: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, D.413 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.413 DMS.20: 8 residues within 4Å: Chain C: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, D.413 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.413 DMS.27: 8 residues within 4Å: Chain D: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, D.413 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.413 Water bridges: D:H.332, D:H.332 DMS.34: 8 residues within 4Å: Chain E: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, D.413 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.413 Water bridges: E:H.332, E:H.332 DMS.41: 8 residues within 4Å: Chain F: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, D.413 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:D.413 Water bridges: F:H.332, F:H.332

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pang, A.H. et al., Discovery and Mechanistic Analysis of Structurally Diverse Inhibitors of Acetyltransferase Eis among FDA-Approved Drugs. Biochemistry (2023)

Release Date

2023-02-01

Peptides

N-acetyltransferase Eis: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

N-acetyltransferase Eis

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