SMTL ID : 6vuw.1

Crystal structure of Eis from Mycobacterium tuberculosis in complex with inhibitor SGT368

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.87 Å

Oligo State

homo-hexamer

Ligands

6 x RNM: (7R)-7-methyl-2-({[(3R)-1-methylpiperidin-3-yl]methyl}sulfanyl)-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4-amine(Non-covalent)

RNM.1: 12 residues within 4Å: Chain A: W.33, D.46, I.48, A.53, W.56, R.57, L.83, M.85, S.103, F.104, E.421, F.422 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.33, A:A.53, A:W.56, A:R.57, A:F.104, A:F.104, A:E.421 Hydrogen bonds: A:S.103, A:F.422 Salt bridges: A:D.46 pi-Stacking: A:W.56, A:W.56, A:W.56 RNM.8: 12 residues within 4Å: Chain B: W.33, D.46, I.48, A.53, W.56, R.57, L.83, M.85, S.103, F.104, E.421, F.422 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.33, B:A.53, B:W.56, B:R.57, B:F.104, B:F.104, B:E.421 Hydrogen bonds: B:S.103, B:F.422 Salt bridges: B:D.46 pi-Stacking: B:W.56, B:W.56, B:W.56 RNM.15: 12 residues within 4Å: Chain C: W.33, D.46, I.48, A.53, W.56, R.57, L.83, M.85, S.103, F.104, E.421, F.422 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:W.33, C:A.53, C:W.56, C:R.57, C:F.104, C:F.104, C:E.421 Hydrogen bonds: C:S.103, C:F.422 Salt bridges: C:D.46 pi-Stacking: C:W.56, C:W.56, C:W.56 RNM.22: 12 residues within 4Å: Chain D: W.33, D.46, I.48, A.53, W.56, R.57, L.83, M.85, S.103, F.104, E.421, F.422 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:W.33, D:A.53, D:W.56, D:R.57, D:F.104, D:F.104, D:E.421 Hydrogen bonds: D:S.103, D:F.422, D:F.422 Salt bridges: D:D.46 pi-Stacking: D:W.56, D:W.56, D:W.56 RNM.29: 12 residues within 4Å: Chain E: W.33, D.46, I.48, A.53, W.56, R.57, L.83, M.85, S.103, F.104, E.421, F.422 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:W.33, E:A.53, E:W.56, E:R.57, E:F.104, E:F.104, E:E.421 Hydrogen bonds: E:S.103, E:F.422, E:F.422 Salt bridges: E:D.46 pi-Stacking: E:W.56, E:W.56, E:W.56 RNM.36: 12 residues within 4Å: Chain F: W.33, D.46, I.48, A.53, W.56, R.57, L.83, M.85, S.103, F.104, E.421, F.422 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:W.33, F:A.53, F:W.56, F:R.57, F:F.104, F:F.104, F:E.421 Hydrogen bonds: F:S.103, F:F.422, F:F.422 Salt bridges: F:D.46 pi-Stacking: F:W.56, F:W.56, F:W.56

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: W.202, L.261, A.263, H.269, T.289, H.290, D.293, P.294, Q.417 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.202, A:A.263, A:T.289 Water bridges: A:L.261, A:T.289, A:T.289, A:D.293 GOL.3: 5 residues within 4Å: Chain A: H.125, A.129, R.317, M.319, R.373 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.125, A:R.317, A:R.317, A:R.373 Water bridges: A:R.373 GOL.9: 9 residues within 4Å: Chain B: W.202, L.261, A.263, H.269, T.289, H.290, D.293, P.294, Q.417 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:W.202, B:A.263, B:T.289 Water bridges: B:L.261, B:T.289, B:T.289, B:D.293 GOL.10: 5 residues within 4Å: Chain B: H.125, A.129, R.317, M.319, R.373 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.125, B:R.317, B:R.317, B:R.373 Water bridges: B:R.373 GOL.16: 9 residues within 4Å: Chain C: W.202, L.261, A.263, H.269, T.289, H.290, D.293, P.294, Q.417 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:W.202, C:A.263, C:T.289 Water bridges: C:L.261, C:T.289, C:T.289, C:D.293 GOL.17: 5 residues within 4Å: Chain C: H.125, A.129, R.317, M.319, R.373 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.125, C:R.317, C:R.317, C:R.373 Water bridges: C:R.373 GOL.23: 9 residues within 4Å: Chain D: W.202, L.261, A.263, H.269, T.289, H.290, D.293, P.294, Q.417 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:W.202, D:A.263 Water bridges: D:T.289, D:T.289, D:D.293, D:D.293 GOL.24: 5 residues within 4Å: Chain D: H.125, A.129, R.317, M.319, R.373 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:H.125, D:R.317, D:R.317, D:R.373 Water bridges: D:R.373 GOL.30: 9 residues within 4Å: Chain E: W.202, L.261, A.263, H.269, T.289, H.290, D.293, P.294, Q.417 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:W.202, E:A.263 Water bridges: E:T.289, E:T.289, E:D.293, E:D.293 GOL.31: 5 residues within 4Å: Chain E: H.125, A.129, R.317, M.319, R.373 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:H.125, E:R.317, E:R.317, E:R.373 Water bridges: E:R.373 GOL.37: 9 residues within 4Å: Chain F: W.202, L.261, A.263, H.269, T.289, H.290, D.293, P.294, Q.417 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:W.202, F:A.263 Water bridges: F:T.289, F:T.289, F:D.293, F:D.293 GOL.38: 5 residues within 4Å: Chain F: H.125, A.129, R.317, M.319, R.373 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:H.125, F:R.317, F:R.317, F:R.373 Water bridges: F:R.373

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

SO4.4: 7 residues within 4Å: Chain A: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: NA.7 Ligand excluded by PLIP SO4.5: 6 residues within 4Å: Chain A: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.6: 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 SO4.11: 7 residues within 4Å: Chain B: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: NA.14 Ligand excluded by PLIP SO4.12: 6 residues within 4Å: Chain B: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.13: 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 SO4.18: 7 residues within 4Å: Chain C: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: NA.21 Ligand excluded by PLIP SO4.19: 6 residues within 4Å: Chain C: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.20: 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 SO4.25: 7 residues within 4Å: Chain D: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: NA.28 Ligand excluded by PLIP SO4.26: 6 residues within 4Å: Chain D: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.27: 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 SO4.32: 7 residues within 4Å: Chain E: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: NA.35 Ligand excluded by PLIP SO4.33: 6 residues within 4Å: Chain E: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.34: 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 SO4.39: 7 residues within 4Å: Chain F: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: NA.42 Ligand excluded by PLIP SO4.40: 6 residues within 4Å: Chain F: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.41: 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

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

NA.7: 6 residues within 4Å: Chain A: T.156, L.157, H.290, Q.417, T.418 Ligands: SO4.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.156, A:T.156, A:T.418 NA.14: 6 residues within 4Å: Chain B: T.156, L.157, H.290, Q.417, T.418 Ligands: SO4.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.156, B:T.418, B:T.418 NA.21: 6 residues within 4Å: Chain C: T.156, L.157, H.290, Q.417, T.418 Ligands: SO4.18 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.156, C:T.418, C:T.418 NA.28: 6 residues within 4Å: Chain D: T.156, L.157, H.290, Q.417, T.418 Ligands: SO4.25 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.156, D:T.418, D:T.418, D:T.418 NA.35: 6 residues within 4Å: Chain E: T.156, L.157, H.290, Q.417, T.418 Ligands: SO4.32 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.156, E:T.156, E:T.418, E:T.418 NA.42: 6 residues within 4Å: Chain F: T.156, L.157, H.290, Q.417, T.418 Ligands: SO4.39 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:T.156, F:T.418, F:T.418, F:T.418

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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