SMTL ID : 6vur.1

Crystal structure of Eis from Mycobacterium tuberculosis in complex with inhibitor SGT366

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

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

ROG.1: 11 residues within 4Å: Chain A: D.46, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.56, A:R.57, A:V.60, A:L.83, A:L.83, 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 ROG.15: 11 residues within 4Å: Chain B: D.46, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:W.56, B:R.57, B:V.60, B:L.83, B:L.83, 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 ROG.29: 11 residues within 4Å: Chain C: D.46, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:W.56, C:R.57, C:V.60, C:L.83, C:L.83, 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 ROG.43: 11 residues within 4Å: Chain D: D.46, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:W.56, D:R.57, D:V.60, D:L.83, D:L.83, 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 ROG.57: 11 residues within 4Å: Chain E: D.46, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:W.56, E:R.57, E:V.60, E:L.83, E:L.83, 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 ROG.71: 11 residues within 4Å: Chain F: D.46, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:W.56, F:R.57, F:V.60, F:L.83, F:L.83, 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

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

SO4.2: 6 residues within 4Å: Chain A: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.3: 8 residues within 4Å: Chain A: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, D.413 Ligand excluded by PLIP SO4.10: 8 residues within 4Å: Chain A: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.7, NA.9 Ligand excluded by PLIP SO4.16: 6 residues within 4Å: Chain B: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.17: 8 residues within 4Å: Chain B: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, D.413 Ligand excluded by PLIP SO4.24: 8 residues within 4Å: Chain B: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.21, NA.23 Ligand excluded by PLIP SO4.30: 6 residues within 4Å: Chain C: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.31: 8 residues within 4Å: Chain C: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, D.413 Ligand excluded by PLIP SO4.38: 8 residues within 4Å: Chain C: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.35, NA.37 Ligand excluded by PLIP SO4.44: 6 residues within 4Å: Chain D: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.45: 8 residues within 4Å: Chain D: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, D.413 Ligand excluded by PLIP SO4.52: 8 residues within 4Å: Chain D: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.49, NA.51 Ligand excluded by PLIP SO4.58: 6 residues within 4Å: Chain E: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.59: 8 residues within 4Å: Chain E: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, D.413 Ligand excluded by PLIP SO4.66: 8 residues within 4Å: Chain E: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.63, NA.65 Ligand excluded by PLIP SO4.72: 6 residues within 4Å: Chain F: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.73: 8 residues within 4Å: Chain F: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, D.413 Ligand excluded by PLIP SO4.80: 8 residues within 4Å: Chain F: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.77, NA.79 Ligand excluded by PLIP

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: H.125, R.317, M.319, R.373 Ligand excluded by PLIP GOL.5: 9 residues within 4Å: Chain A: F.44, S.103, F.104, V.105, L.138, H.139, A.140, S.141, Y.146 Ligand excluded by PLIP GOL.13: 5 residues within 4Å: Chain A: P.61, T.62, Y.84, S.131, Y.133 Ligand excluded by PLIP GOL.18: 4 residues within 4Å: Chain B: H.125, R.317, M.319, R.373 Ligand excluded by PLIP GOL.19: 9 residues within 4Å: Chain B: F.44, S.103, F.104, V.105, L.138, H.139, A.140, S.141, Y.146 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain B: P.61, T.62, Y.84, S.131, Y.133 Ligand excluded by PLIP GOL.32: 4 residues within 4Å: Chain C: H.125, R.317, M.319, R.373 Ligand excluded by PLIP GOL.33: 9 residues within 4Å: Chain C: F.44, S.103, F.104, V.105, L.138, H.139, A.140, S.141, Y.146 Ligand excluded by PLIP GOL.41: 5 residues within 4Å: Chain C: P.61, T.62, Y.84, S.131, Y.133 Ligand excluded by PLIP GOL.46: 4 residues within 4Å: Chain D: H.125, R.317, M.319, R.373 Ligand excluded by PLIP GOL.47: 9 residues within 4Å: Chain D: F.44, S.103, F.104, V.105, L.138, H.139, A.140, S.141, Y.146 Ligand excluded by PLIP GOL.55: 5 residues within 4Å: Chain D: P.61, T.62, Y.84, S.131, Y.133 Ligand excluded by PLIP GOL.60: 4 residues within 4Å: Chain E: H.125, R.317, M.319, R.373 Ligand excluded by PLIP GOL.61: 9 residues within 4Å: Chain E: F.44, S.103, F.104, V.105, L.138, H.139, A.140, S.141, Y.146 Ligand excluded by PLIP GOL.69: 5 residues within 4Å: Chain E: P.61, T.62, Y.84, S.131, Y.133 Ligand excluded by PLIP GOL.74: 4 residues within 4Å: Chain F: H.125, R.317, M.319, R.373 Ligand excluded by PLIP GOL.75: 9 residues within 4Å: Chain F: F.44, S.103, F.104, V.105, L.138, H.139, A.140, S.141, Y.146 Ligand excluded by PLIP GOL.83: 5 residues within 4Å: Chain F: P.61, T.62, Y.84, S.131, Y.133 Ligand excluded by PLIP

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

PEG.6: 6 residues within 4Å: Chain A: T.156, P.291, Q.292, A.383, V.416 Ligands: PEG.62 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.156, A:T.156 Water bridges: A:T.156, A:Q.292, A:V.416 PEG.7: 10 residues within 4Å: Chain A: L.261, H.269, I.287, I.288, T.289, H.290, D.293, P.294, Q.417 Ligands: SO4.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.288, A:T.289 PEG.20: 6 residues within 4Å: Chain B: T.156, P.291, Q.292, A.383, V.416 Ligands: PEG.48 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.156, B:T.156 Water bridges: B:T.156, B:Q.292, B:V.416 PEG.21: 10 residues within 4Å: Chain B: L.261, H.269, I.287, I.288, T.289, H.290, D.293, P.294, Q.417 Ligands: SO4.24 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.288, B:T.289 PEG.34: 6 residues within 4Å: Chain C: T.156, P.291, Q.292, A.383, V.416 Ligands: PEG.76 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.156, C:T.156 Water bridges: C:T.156, C:Q.292, C:V.416 PEG.35: 10 residues within 4Å: Chain C: L.261, H.269, I.287, I.288, T.289, H.290, D.293, P.294, Q.417 Ligands: SO4.38 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.288, C:T.289 PEG.48: 6 residues within 4Å: Chain D: T.156, P.291, Q.292, A.383, V.416 Ligands: PEG.20 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.156 Water bridges: D:T.156, D:T.156, D:Q.292, D:V.416 PEG.49: 10 residues within 4Å: Chain D: L.261, H.269, I.287, I.288, T.289, H.290, D.293, P.294, Q.417 Ligands: SO4.52 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:I.288 PEG.62: 6 residues within 4Å: Chain E: T.156, P.291, Q.292, A.383, V.416 Ligands: PEG.6 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:T.156 Water bridges: E:T.156, E:T.156, E:Q.292, E:V.416 PEG.63: 10 residues within 4Å: Chain E: L.261, H.269, I.287, I.288, T.289, H.290, D.293, P.294, Q.417 Ligands: SO4.66 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:I.288 PEG.76: 6 residues within 4Å: Chain F: T.156, P.291, Q.292, A.383, V.416 Ligands: PEG.34 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:T.156 Water bridges: F:T.156, F:T.156, F:Q.292, F:V.416 PEG.77: 10 residues within 4Å: Chain F: L.261, H.269, I.287, I.288, T.289, H.290, D.293, P.294, Q.417 Ligands: SO4.80 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:I.288

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

NA.8: 7 residues within 4Å: Chain A: A.154, S.378, L.379, Y.380, L.381, G.382, A.383 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.379, A:L.381, A:G.382, A:A.383 NA.9: 6 residues within 4Å: Chain A: T.156, T.289, H.290, Q.417, T.418 Ligands: SO4.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.156, A:T.418, A:T.418 Water bridges: A:T.156 NA.22: 7 residues within 4Å: Chain B: A.154, S.378, L.379, Y.380, L.381, G.382, A.383 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.154, B:L.381, B:G.382, B:A.383 NA.23: 6 residues within 4Å: Chain B: T.156, T.289, H.290, Q.417, T.418 Ligands: SO4.24 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.289, B:T.418, B:T.418 Water bridges: B:T.156 NA.36: 7 residues within 4Å: Chain C: A.154, S.378, L.379, Y.380, L.381, G.382, A.383 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.378, C:L.381, C:G.382, C:A.383 NA.37: 6 residues within 4Å: Chain C: T.156, T.289, H.290, Q.417, T.418 Ligands: SO4.38 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.156, C:T.418, C:T.418 Water bridges: C:T.156 NA.50: 7 residues within 4Å: Chain D: A.154, S.378, L.379, Y.380, L.381, G.382, A.383 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:L.379, D:L.381, D:G.382, D:A.383 NA.51: 6 residues within 4Å: Chain D: T.156, T.289, H.290, Q.417, T.418 Ligands: SO4.52 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.418, D:T.418 Water bridges: D:T.156 NA.64: 7 residues within 4Å: Chain E: A.154, S.378, L.379, Y.380, L.381, G.382, A.383 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:L.379, E:L.381, E:G.382, E:A.383 NA.65: 6 residues within 4Å: Chain E: T.156, T.289, H.290, Q.417, T.418 Ligands: SO4.66 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.418, E:T.418 Water bridges: E:T.156 NA.78: 7 residues within 4Å: Chain F: A.154, S.378, L.379, Y.380, L.381, G.382, A.383 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:L.379, F:L.381, F:G.382, F:A.383 NA.79: 6 residues within 4Å: Chain F: T.156, T.289, H.290, Q.417, T.418 Ligands: SO4.80 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:T.156, F:T.418 Water bridges: F:T.156

18 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 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 CL.12: 7 residues within 4Å: Chain A: H.170, D.172, A.173, H.297, L.298 Chain E: A.392, R.394 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: G.115, L.116, L.117, R.118 Ligand excluded by PLIP CL.25: 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 CL.26: 7 residues within 4Å: Chain B: H.170, D.172, A.173, H.297, L.298 Chain D: A.392, R.394 Ligand excluded by PLIP CL.28: 4 residues within 4Å: Chain B: G.115, L.116, L.117, R.118 Ligand excluded by PLIP CL.39: 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 CL.40: 7 residues within 4Å: Chain C: H.170, D.172, A.173, H.297, L.298 Chain F: A.392, R.394 Ligand excluded by PLIP CL.42: 4 residues within 4Å: Chain C: G.115, L.116, L.117, R.118 Ligand excluded by PLIP CL.53: 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 CL.54: 7 residues within 4Å: Chain B: A.392, R.394 Chain D: H.170, D.172, A.173, H.297, L.298 Ligand excluded by PLIP CL.56: 4 residues within 4Å: Chain D: G.115, L.116, L.117, R.118 Ligand excluded by PLIP CL.67: 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 CL.68: 7 residues within 4Å: Chain A: A.392, R.394 Chain E: H.170, D.172, A.173, H.297, L.298 Ligand excluded by PLIP CL.70: 4 residues within 4Å: Chain E: G.115, L.116, L.117, R.118 Ligand excluded by PLIP CL.81: 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 CL.82: 7 residues within 4Å: Chain C: A.392, R.394 Chain F: H.170, D.172, A.173, H.297, L.298 Ligand excluded by PLIP CL.84: 4 residues within 4Å: Chain F: G.115, L.116, L.117, R.118 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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