SMTL ID : 6vut.1

Crystal structure of Eis from Mycobacterium tuberculosis in complex with inhibitor SGT392

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.73 Å

Oligo State

homo-hexamer

Ligands

6 x RN7: 2-[(4-amino-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-2-yl)sulfanyl]-N-[2-(morpholin-4-yl)ethyl]acetamide(Non-covalent)

RN7.1: 12 residues within 4Å: Chain A: D.46, I.48, A.53, W.56, V.60, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: PEG.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.53, A:W.56, A:V.60, A:L.83, A:L.83, A:F.104, A:F.104 Hydrogen bonds: A:S.103, A:F.104, A:F.422 Water bridges: A:E.421 Salt bridges: A:D.46 pi-Stacking: A:W.56, A:W.56 RN7.11: 12 residues within 4Å: Chain B: D.46, I.48, A.53, W.56, V.60, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: PEG.12 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:A.53, B:W.56, B:V.60, B:L.83, B:L.83, B:F.104, B:F.104 Hydrogen bonds: B:S.103, B:F.104, B:F.422 Water bridges: B:E.421 Salt bridges: B:D.46 pi-Stacking: B:W.56, B:W.56 RN7.21: 12 residues within 4Å: Chain C: D.46, I.48, A.53, W.56, V.60, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: PEG.22 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:A.53, C:W.56, C:V.60, C:L.83, C:L.83, C:F.104, C:F.104 Hydrogen bonds: C:S.103, C:F.104, C:F.422 Water bridges: C:E.421 Salt bridges: C:D.46 pi-Stacking: C:W.56, C:W.56 RN7.31: 12 residues within 4Å: Chain D: D.46, I.48, A.53, W.56, V.60, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: PEG.32 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:A.53, D:W.56, D:V.60, D:L.83, D:L.83, D:F.104, D:F.104 Hydrogen bonds: D:S.103, D:F.104, D:F.422, D:F.422 Salt bridges: D:D.46 pi-Stacking: D:W.56, D:W.56 RN7.41: 12 residues within 4Å: Chain E: D.46, I.48, A.53, W.56, V.60, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: PEG.42 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:A.53, E:W.56, E:V.60, E:L.83, E:L.83, E:F.104, E:F.104 Hydrogen bonds: E:S.103, E:F.104, E:F.422, E:F.422 Salt bridges: E:D.46 pi-Stacking: E:W.56, E:W.56 RN7.51: 12 residues within 4Å: Chain F: D.46, I.48, A.53, W.56, V.60, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: PEG.52 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:A.53, F:W.56, F:V.60, F:L.83, F:L.83, F:F.104, F:F.104 Hydrogen bonds: F:S.103, F:F.104, F:F.422, F:F.422 Salt bridges: F:D.46 pi-Stacking: F:W.56, F:W.56

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

PEG.2: 6 residues within 4Å: Chain A: H.139, A.140, Q.311, E.421, F.422 Ligands: RN7.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.139, A:D.312, A:F.422 Water bridges: A:A.140 PEG.3: 12 residues within 4Å: Chain A: E.260, L.261, R.262, H.269, I.287, I.288, T.289, H.290, D.293, Q.417 Ligands: SO4.5, NA.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.261, A:H.269, A:T.289 PEG.12: 6 residues within 4Å: Chain B: H.139, A.140, Q.311, E.421, F.422 Ligands: RN7.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.139, B:D.312, B:F.422 Water bridges: B:A.140 PEG.13: 12 residues within 4Å: Chain B: E.260, L.261, R.262, H.269, I.287, I.288, T.289, H.290, D.293, Q.417 Ligands: SO4.15, NA.19 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.261, B:H.269, B:T.289 PEG.22: 6 residues within 4Å: Chain C: H.139, A.140, Q.311, E.421, F.422 Ligands: RN7.21 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.139, C:D.312, C:F.422 Water bridges: C:A.140 PEG.23: 12 residues within 4Å: Chain C: E.260, L.261, R.262, H.269, I.287, I.288, T.289, H.290, D.293, Q.417 Ligands: SO4.25, NA.29 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.261, C:H.269, C:T.289 PEG.32: 6 residues within 4Å: Chain D: H.139, A.140, Q.311, E.421, F.422 Ligands: RN7.31 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.312, D:E.421, D:F.422 Water bridges: D:A.140 PEG.33: 12 residues within 4Å: Chain D: E.260, L.261, R.262, H.269, I.287, I.288, T.289, H.290, D.293, Q.417 Ligands: SO4.35, NA.39 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.261 PEG.42: 6 residues within 4Å: Chain E: H.139, A.140, Q.311, E.421, F.422 Ligands: RN7.41 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:D.312, E:E.421, E:F.422 Water bridges: E:A.140 PEG.43: 12 residues within 4Å: Chain E: E.260, L.261, R.262, H.269, I.287, I.288, T.289, H.290, D.293, Q.417 Ligands: SO4.45, NA.49 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:L.261 PEG.52: 6 residues within 4Å: Chain F: H.139, A.140, Q.311, E.421, F.422 Ligands: RN7.51 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:D.312, F:E.421, F:F.422 Water bridges: F:A.140 PEG.53: 12 residues within 4Å: Chain F: E.260, L.261, R.262, H.269, I.287, I.288, T.289, H.290, D.293, Q.417 Ligands: SO4.55, NA.59 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:L.261

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: H.125, R.126, R.317, M.319, R.373 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.317, A:R.317, A:M.319 Water bridges: A:R.126 GOL.14: 5 residues within 4Å: Chain B: H.125, R.126, R.317, M.319, R.373 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.317, B:R.317, B:M.319 Water bridges: B:R.126 GOL.24: 5 residues within 4Å: Chain C: H.125, R.126, R.317, M.319, R.373 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.317, C:R.317, C:M.319 Water bridges: C:R.126 GOL.34: 5 residues within 4Å: Chain D: H.125, R.126, R.317, M.319, R.373 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.317, D:R.317, D:M.319 Water bridges: D:R.126 GOL.44: 5 residues within 4Å: Chain E: H.125, R.126, R.317, M.319, R.373 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.317, E:R.317, E:M.319 Water bridges: E:R.126 GOL.54: 5 residues within 4Å: Chain F: H.125, R.126, R.317, M.319, R.373 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:R.317, F:R.317, F:M.319 Water bridges: F:R.126

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

SO4.5: 7 residues within 4Å: Chain A: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.3 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: W.33, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.7: 9 residues within 4Å: Chain A: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, S.412, D.413 Ligand excluded by PLIP SO4.15: 7 residues within 4Å: Chain B: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.13 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain B: W.33, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.17: 9 residues within 4Å: Chain B: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, S.412, D.413 Ligand excluded by PLIP SO4.25: 7 residues within 4Å: Chain C: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.23 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain C: W.33, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.27: 9 residues within 4Å: Chain C: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, S.412, D.413 Ligand excluded by PLIP SO4.35: 7 residues within 4Å: Chain D: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.33 Ligand excluded by PLIP SO4.36: 5 residues within 4Å: Chain D: W.33, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.37: 9 residues within 4Å: Chain D: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, S.412, D.413 Ligand excluded by PLIP SO4.45: 7 residues within 4Å: Chain E: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.43 Ligand excluded by PLIP SO4.46: 5 residues within 4Å: Chain E: W.33, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.47: 9 residues within 4Å: Chain E: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, S.412, D.413 Ligand excluded by PLIP SO4.55: 7 residues within 4Å: Chain F: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.53 Ligand excluded by PLIP SO4.56: 5 residues within 4Å: Chain F: W.33, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.57: 9 residues within 4Å: Chain F: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, S.412, D.413 Ligand excluded by PLIP

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

NA.8: 8 residues within 4Å: Chain A: R.88, L.89, T.90, V.96, R.203, G.209, L.210, L.211 Ligand excluded by PLIP NA.9: 7 residues within 4Å: Chain A: L.261, H.269, W.273, I.287, T.289, D.293 Ligands: PEG.3 Ligand excluded by PLIP NA.10: 7 residues within 4Å: Chain A: G.150, L.316, R.317, I.318, R.373, D.374, G.377 Ligand excluded by PLIP NA.18: 8 residues within 4Å: Chain B: R.88, L.89, T.90, V.96, R.203, G.209, L.210, L.211 Ligand excluded by PLIP NA.19: 7 residues within 4Å: Chain B: L.261, H.269, W.273, I.287, T.289, D.293 Ligands: PEG.13 Ligand excluded by PLIP NA.20: 7 residues within 4Å: Chain B: G.150, L.316, R.317, I.318, R.373, D.374, G.377 Ligand excluded by PLIP NA.28: 8 residues within 4Å: Chain C: R.88, L.89, T.90, V.96, R.203, G.209, L.210, L.211 Ligand excluded by PLIP NA.29: 7 residues within 4Å: Chain C: L.261, H.269, W.273, I.287, T.289, D.293 Ligands: PEG.23 Ligand excluded by PLIP NA.30: 7 residues within 4Å: Chain C: G.150, L.316, R.317, I.318, R.373, D.374, G.377 Ligand excluded by PLIP NA.38: 8 residues within 4Å: Chain D: R.88, L.89, T.90, V.96, R.203, G.209, L.210, L.211 Ligand excluded by PLIP NA.39: 7 residues within 4Å: Chain D: L.261, H.269, W.273, I.287, T.289, D.293 Ligands: PEG.33 Ligand excluded by PLIP NA.40: 7 residues within 4Å: Chain D: G.150, L.316, R.317, I.318, R.373, D.374, G.377 Ligand excluded by PLIP NA.48: 8 residues within 4Å: Chain E: R.88, L.89, T.90, V.96, R.203, G.209, L.210, L.211 Ligand excluded by PLIP NA.49: 7 residues within 4Å: Chain E: L.261, H.269, W.273, I.287, T.289, D.293 Ligands: PEG.43 Ligand excluded by PLIP NA.50: 7 residues within 4Å: Chain E: G.150, L.316, R.317, I.318, R.373, D.374, G.377 Ligand excluded by PLIP NA.58: 8 residues within 4Å: Chain F: R.88, L.89, T.90, V.96, R.203, G.209, L.210, L.211 Ligand excluded by PLIP NA.59: 7 residues within 4Å: Chain F: L.261, H.269, W.273, I.287, T.289, D.293 Ligands: PEG.53 Ligand excluded by PLIP NA.60: 7 residues within 4Å: Chain F: G.150, L.316, R.317, I.318, R.373, D.374, G.377 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Punetha, A. et al., Structure-Guided Optimization of Inhibitors of Acetyltransferase Eis fromMycobacterium tuberculosis. Acs Chem.Biol. (2020)

Release Date

2020-06-03

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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