SMTL ID : 6vv1.1

Crystal structure of Eis from Mycobacterium tuberculosis in complex with inhibitor SGT384

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-hexamer

Ligands

6 x RMJ: 2-[(4-amino-6,7-dihydro-5H-cyclopenta[4,5]thieno[2,3-d]pyrimidin-2-yl)sulfanyl]-N-[2-(piperidin-1-yl)ethyl]acetamide(Non-covalent)

RMJ.1: 10 residues within 4Å: Chain A: F.44, D.46, A.53, W.56, L.83, M.85, S.103, F.104, E.421, F.422 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.44, A:W.56, A:L.83, A:L.83, A:F.104, A:F.104 Hydrogen bonds: A:S.103, A:E.421, A:F.422 Salt bridges: A:D.46 pi-Stacking: A:W.56, A:W.56 RMJ.13: 10 residues within 4Å: Chain B: F.44, D.46, A.53, W.56, L.83, M.85, S.103, F.104, E.421, F.422 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.44, B:W.56, B:L.83, B:L.83, B:F.104, B:F.104 Hydrogen bonds: B:S.103, B:E.421, B:F.422 Salt bridges: B:D.46 pi-Stacking: B:W.56, B:W.56 RMJ.25: 10 residues within 4Å: Chain C: F.44, D.46, A.53, W.56, L.83, M.85, S.103, F.104, E.421, F.422 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:F.44, C:W.56, C:L.83, C:L.83, C:F.104, C:F.104 Hydrogen bonds: C:S.103, C:E.421, C:F.422 Salt bridges: C:D.46 pi-Stacking: C:W.56, C:W.56 RMJ.37: 10 residues within 4Å: Chain D: F.44, D.46, A.53, W.56, L.83, M.85, S.103, F.104, E.421, F.422 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:F.44, D:W.56, D:L.83, D:L.83, D:F.104, D:F.104 Hydrogen bonds: D:S.103, D:E.421, D:F.422, D:F.422 Water bridges: D:E.421, D:E.421 Salt bridges: D:D.46 pi-Stacking: D:W.56, D:W.56 RMJ.49: 10 residues within 4Å: Chain E: F.44, D.46, A.53, W.56, L.83, M.85, S.103, F.104, E.421, F.422 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:F.44, E:W.56, E:L.83, E:L.83, E:F.104, E:F.104 Hydrogen bonds: E:S.103, E:E.421, E:F.422, E:F.422 Water bridges: E:E.421, E:E.421 Salt bridges: E:D.46 pi-Stacking: E:W.56, E:W.56 RMJ.61: 10 residues within 4Å: Chain F: F.44, D.46, A.53, W.56, L.83, M.85, S.103, F.104, E.421, F.422 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:F.44, F:W.56, F:L.83, F:L.83, F:F.104, F:F.104 Hydrogen bonds: F:S.103, F:E.421, F:F.422, F:F.422 Water bridges: F:E.421, F:E.421 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: E.196, A.197, E.200, R.212, Q.214 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.214 Water bridges: A:E.200, A:E.200 PEG.3: 11 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: DMS.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.261, A:T.289 Water bridges: A:A.263, A:A.263, A:Q.417, A:Q.417 PEG.14: 6 residues within 4Å: Chain B: E.196, A.197, E.200, R.212, Q.214 Ligands: GOL.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.214 Water bridges: B:E.200, B:E.200 PEG.15: 11 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: DMS.23 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.261, B:T.289 Water bridges: B:A.263, B:A.263, B:Q.417, B:Q.417 PEG.26: 6 residues within 4Å: Chain C: E.196, A.197, E.200, R.212, Q.214 Ligands: GOL.28 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.214 Water bridges: C:E.200, C:E.200 PEG.27: 11 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: DMS.35 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:L.261, C:T.289 Water bridges: C:A.263, C:A.263, C:Q.417, C:Q.417 PEG.38: 6 residues within 4Å: Chain D: E.196, A.197, E.200, R.212, Q.214 Ligands: GOL.40 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.214 Water bridges: D:E.200 PEG.39: 11 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: DMS.47 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:L.261 Water bridges: D:A.263, D:A.263, D:Q.417, D:Q.417 PEG.50: 6 residues within 4Å: Chain E: E.196, A.197, E.200, R.212, Q.214 Ligands: GOL.52 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.214 Water bridges: E:E.200 PEG.51: 11 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: DMS.59 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:L.261 Water bridges: E:A.263, E:A.263, E:Q.417, E:Q.417 PEG.62: 6 residues within 4Å: Chain F: E.196, A.197, E.200, R.212, Q.214 Ligands: GOL.64 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Q.214 Water bridges: F:E.200 PEG.63: 11 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: DMS.71 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:L.261 Water bridges: F:A.263, F:A.263, F:Q.417, F:Q.417

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain A: Q.214 Ligands: PEG.2 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: R.57, T.58, V.60, P.61 Ligand excluded by PLIP GOL.16: 2 residues within 4Å: Chain B: Q.214 Ligands: PEG.14 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain B: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain B: R.57, T.58, V.60, P.61 Ligand excluded by PLIP GOL.28: 2 residues within 4Å: Chain C: Q.214 Ligands: PEG.26 Ligand excluded by PLIP GOL.29: 6 residues within 4Å: Chain C: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.32: 4 residues within 4Å: Chain C: R.57, T.58, V.60, P.61 Ligand excluded by PLIP GOL.40: 2 residues within 4Å: Chain D: Q.214 Ligands: PEG.38 Ligand excluded by PLIP GOL.41: 6 residues within 4Å: Chain D: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.44: 4 residues within 4Å: Chain D: R.57, T.58, V.60, P.61 Ligand excluded by PLIP GOL.52: 2 residues within 4Å: Chain E: Q.214 Ligands: PEG.50 Ligand excluded by PLIP GOL.53: 6 residues within 4Å: Chain E: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.56: 4 residues within 4Å: Chain E: R.57, T.58, V.60, P.61 Ligand excluded by PLIP GOL.64: 2 residues within 4Å: Chain F: Q.214 Ligands: PEG.62 Ligand excluded by PLIP GOL.65: 6 residues within 4Å: Chain F: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.68: 4 residues within 4Å: Chain F: R.57, T.58, V.60, P.61 Ligand excluded by PLIP

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

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 SO4.7: 6 residues within 4Å: Chain A: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.10: 7 residues within 4Å: Chain A: A.367, E.368, I.369, E.370, R.396, T.397, K.398 Ligand excluded by PLIP SO4.18: 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 SO4.19: 6 residues within 4Å: Chain B: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.22: 7 residues within 4Å: Chain B: A.367, E.368, I.369, E.370, R.396, T.397, K.398 Ligand excluded by PLIP SO4.30: 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 SO4.31: 6 residues within 4Å: Chain C: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.34: 7 residues within 4Å: Chain C: A.367, E.368, I.369, E.370, R.396, T.397, K.398 Ligand excluded by PLIP SO4.42: 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 SO4.43: 6 residues within 4Å: Chain D: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.46: 7 residues within 4Å: Chain D: A.367, E.368, I.369, E.370, R.396, T.397, K.398 Ligand excluded by PLIP SO4.54: 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: 6 residues within 4Å: Chain E: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.58: 7 residues within 4Å: Chain E: A.367, E.368, I.369, E.370, R.396, T.397, K.398 Ligand excluded by PLIP SO4.66: 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 SO4.67: 6 residues within 4Å: Chain F: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.70: 7 residues within 4Å: Chain F: A.367, E.368, I.369, E.370, R.396, T.397, K.398 Ligand excluded by PLIP

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

DMS.9: 2 residues within 4Å: Chain A: E.159, W.309 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:E.159 pi-Cation interactions: A:W.309, A:W.309 DMS.11: 7 residues within 4Å: Chain A: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.418, A:T.418 DMS.21: 2 residues within 4Å: Chain B: E.159, W.309 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:E.159 pi-Cation interactions: B:W.309, B:W.309 DMS.23: 7 residues within 4Å: Chain B: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.418, B:T.418 DMS.33: 2 residues within 4Å: Chain C: E.159, W.309 3 PLIP interactions: 3 interactions with chain C Salt bridges: C:E.159 pi-Cation interactions: C:W.309, C:W.309 DMS.35: 7 residues within 4Å: Chain C: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.27 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.418, C:T.418 DMS.45: 2 residues within 4Å: Chain D: E.159, W.309 3 PLIP interactions: 3 interactions with chain D Salt bridges: D:E.159 pi-Cation interactions: D:W.309, D:W.309 DMS.47: 7 residues within 4Å: Chain D: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.39 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.418 DMS.57: 2 residues within 4Å: Chain E: E.159, W.309 3 PLIP interactions: 3 interactions with chain E Salt bridges: E:E.159 pi-Cation interactions: E:W.309, E:W.309 DMS.59: 7 residues within 4Å: Chain E: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.51 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.418 DMS.69: 2 residues within 4Å: Chain F: E.159, W.309 3 PLIP interactions: 3 interactions with chain F Salt bridges: F:E.159 pi-Cation interactions: F:W.309, F:W.309 DMS.71: 7 residues within 4Å: Chain F: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.63 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:T.418

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

NA.12: 2 residues within 4Å: Chain A: S.338, E.368 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.368 NA.24: 2 residues within 4Å: Chain B: S.338, E.368 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.368 NA.36: 2 residues within 4Å: Chain C: S.338, E.368 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.338 NA.48: 2 residues within 4Å: Chain D: S.338, E.368 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.338 NA.60: 2 residues within 4Å: Chain E: S.338, E.368 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.368 NA.72: 2 residues within 4Å: Chain F: S.338, E.368 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.338

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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