SMTL ID : 8f4z.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

6 x CLQ: N4-(7-CHLORO-QUINOLIN-4-YL)-N1,N1-DIETHYL-PENTANE-1,4-DIAMINE(Non-covalent)

CLQ.1: 11 residues within 4Å: Chain A: F.44, D.46, S.52, A.53, W.56, L.83, S.103, F.104, E.421, F.422 Ligands: GOL.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.44, A:F.44, A:A.53, A:W.56, A:F.104, A:E.421 Hydrogen bonds: A:F.422 Salt bridges: A:D.46 pi-Stacking: A:W.56, A:W.56 CLQ.8: 11 residues within 4Å: Chain B: F.44, D.46, S.52, A.53, W.56, L.83, S.103, F.104, E.421, F.422 Ligands: GOL.10 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.44, B:F.44, B:A.53, B:W.56, B:F.104, B:E.421 Hydrogen bonds: B:F.422 Salt bridges: B:D.46 pi-Stacking: B:W.56, B:W.56 CLQ.15: 11 residues within 4Å: Chain C: F.44, D.46, S.52, A.53, W.56, L.83, S.103, F.104, E.421, F.422 Ligands: GOL.17 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.44, C:F.44, C:A.53, C:W.56, C:F.104, C:E.421 Hydrogen bonds: C:F.422 Salt bridges: C:D.46 pi-Stacking: C:W.56, C:W.56 CLQ.22: 11 residues within 4Å: Chain D: F.44, D.46, S.52, A.53, W.56, L.83, S.103, F.104, E.421, F.422 Ligands: GOL.24 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:F.44, D:F.44, D:A.53, D:W.56, D:F.104, D:E.421 Hydrogen bonds: D:F.422, D:F.422 Water bridges: D:E.421 Salt bridges: D:D.46 pi-Stacking: D:W.56, D:W.56 CLQ.29: 11 residues within 4Å: Chain E: F.44, D.46, S.52, A.53, W.56, L.83, S.103, F.104, E.421, F.422 Ligands: GOL.31 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:F.44, E:F.44, E:A.53, E:W.56, E:F.104, E:E.421 Hydrogen bonds: E:F.422, E:F.422 Water bridges: E:E.421 Salt bridges: E:D.46 pi-Stacking: E:W.56, E:W.56 CLQ.36: 11 residues within 4Å: Chain F: F.44, D.46, S.52, A.53, W.56, L.83, S.103, F.104, E.421, F.422 Ligands: GOL.38 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:F.44, F:F.44, F:A.53, F:W.56, F:F.104, F:E.421 Hydrogen bonds: F:F.422, F:F.422 Water bridges: F:E.421 Salt bridges: F:D.46 pi-Stacking: F:W.56, F:W.56

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: H.125, R.126, A.129, R.317, M.319, R.373 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.317, A:R.317, A:M.319, A:R.373 Water bridges: A:R.126 GOL.3: 10 residues within 4Å: Chain A: F.44, L.102, S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligands: CLQ.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.104, A:V.105, A:S.141, A:Y.146 Water bridges: A:F.422, A:F.422 GOL.9: 6 residues within 4Å: Chain B: H.125, R.126, A.129, R.317, M.319, R.373 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.317, B:R.317, B:M.319, B:R.373 Water bridges: B:R.126 GOL.10: 10 residues within 4Å: Chain B: F.44, L.102, S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligands: CLQ.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:F.104, B:V.105, B:S.141, B:Y.146 Water bridges: B:F.422, B:F.422 GOL.16: 6 residues within 4Å: Chain C: H.125, R.126, A.129, R.317, M.319, R.373 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.317, C:R.317, C:M.319, C:R.373 Water bridges: C:R.126 GOL.17: 10 residues within 4Å: Chain C: F.44, L.102, S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligands: CLQ.15 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:F.104, C:V.105, C:S.141, C:Y.146 Water bridges: C:F.422, C:F.422 GOL.23: 6 residues within 4Å: Chain D: H.125, R.126, A.129, R.317, M.319, R.373 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.317, D:R.317, D:M.319, D:R.373 Water bridges: D:R.126 GOL.24: 10 residues within 4Å: Chain D: F.44, L.102, S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligands: CLQ.22 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:F.104, D:V.105, D:S.141, D:Y.146, D:Y.146 Water bridges: D:F.422, D:F.422 GOL.30: 6 residues within 4Å: Chain E: H.125, R.126, A.129, R.317, M.319, R.373 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:R.317, E:R.317, E:M.319, E:R.373 Water bridges: E:R.126 GOL.31: 10 residues within 4Å: Chain E: F.44, L.102, S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligands: CLQ.29 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:F.104, E:V.105, E:S.141, E:Y.146, E:Y.146 Water bridges: E:F.422, E:F.422 GOL.37: 6 residues within 4Å: Chain F: H.125, R.126, A.129, R.317, M.319, R.373 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:R.317, F:R.317, F:M.319, F:R.373 Water bridges: F:R.126 GOL.38: 10 residues within 4Å: Chain F: F.44, L.102, S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligands: CLQ.36 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:F.104, F:V.105, F:S.141, F:Y.146, F:Y.146 Water bridges: F:F.422, F:F.422

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

PEG.4: 5 residues within 4Å: Chain A: T.58, L.59, V.60, P.61, D.86 Ligand excluded by PLIP 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: PEG.6 Ligand excluded by PLIP PEG.6: 8 residues within 4Å: Chain A: A.263, V.264, T.265, A.266, H.269, P.294 Chain E: A.391 Ligands: PEG.5 Ligand excluded by PLIP PEG.7: 6 residues within 4Å: Chain A: S.259, R.262, I.288, T.418, A.419, F.420 Ligand excluded by PLIP PEG.11: 5 residues within 4Å: Chain B: T.58, L.59, V.60, P.61, D.86 Ligand excluded by PLIP 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: PEG.13 Ligand excluded by PLIP PEG.13: 8 residues within 4Å: Chain B: A.263, V.264, T.265, A.266, H.269, P.294 Chain D: A.391 Ligands: PEG.12 Ligand excluded by PLIP PEG.14: 6 residues within 4Å: Chain B: S.259, R.262, I.288, T.418, A.419, F.420 Ligand excluded by PLIP PEG.18: 5 residues within 4Å: Chain C: T.58, L.59, V.60, P.61, D.86 Ligand excluded by PLIP 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: PEG.20 Ligand excluded by PLIP PEG.20: 8 residues within 4Å: Chain C: A.263, V.264, T.265, A.266, H.269, P.294 Chain F: A.391 Ligands: PEG.19 Ligand excluded by PLIP PEG.21: 6 residues within 4Å: Chain C: S.259, R.262, I.288, T.418, A.419, F.420 Ligand excluded by PLIP PEG.25: 5 residues within 4Å: Chain D: T.58, L.59, V.60, P.61, D.86 Ligand excluded by PLIP 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: PEG.27 Ligand excluded by PLIP PEG.27: 8 residues within 4Å: Chain B: A.391 Chain D: A.263, V.264, T.265, A.266, H.269, P.294 Ligands: PEG.26 Ligand excluded by PLIP PEG.28: 6 residues within 4Å: Chain D: S.259, R.262, I.288, T.418, A.419, F.420 Ligand excluded by PLIP PEG.32: 5 residues within 4Å: Chain E: T.58, L.59, V.60, P.61, D.86 Ligand excluded by PLIP 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: PEG.34 Ligand excluded by PLIP PEG.34: 8 residues within 4Å: Chain A: A.391 Chain E: A.263, V.264, T.265, A.266, H.269, P.294 Ligands: PEG.33 Ligand excluded by PLIP PEG.35: 6 residues within 4Å: Chain E: S.259, R.262, I.288, T.418, A.419, F.420 Ligand excluded by PLIP PEG.39: 5 residues within 4Å: Chain F: T.58, L.59, V.60, P.61, D.86 Ligand excluded by PLIP 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: PEG.41 Ligand excluded by PLIP PEG.41: 8 residues within 4Å: Chain C: A.391 Chain F: A.263, V.264, T.265, A.266, H.269, P.294 Ligands: PEG.40 Ligand excluded by PLIP PEG.42: 6 residues within 4Å: Chain F: S.259, R.262, I.288, T.418, A.419, F.420 Ligand excluded by PLIP

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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