SMTL ID : 6vuu.1

Crystal structure of Eis from Mycobacterium tuberculosis in complex with inhibitor SGT1347

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-hexamer

Ligands

6 x RNJ: (7S)-7-methyl-2-{[3-(piperidin-1-yl)propyl]sulfanyl}-7,8-dihydro[1]benzothieno[2,3-d]pyrimidin-4-amine(Non-covalent)

RNJ.1: 14 residues within 4Å: Chain A: W.33, D.46, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, H.139, E.421, F.422 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.33, A:A.53, A:W.56, A:R.57, A:V.60, A:F.104, A:F.104, A:H.139 Hydrogen bonds: A:S.103, A:F.422 Salt bridges: A:D.46 pi-Stacking: A:W.56, A:W.56, A:W.56 RNJ.9: 14 residues within 4Å: Chain B: W.33, D.46, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, H.139, E.421, F.422 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:W.33, B:A.53, B:W.56, B:R.57, B:V.60, B:F.104, B:F.104, B:H.139 Hydrogen bonds: B:S.103, B:F.422 Salt bridges: B:D.46 pi-Stacking: B:W.56, B:W.56, B:W.56 RNJ.17: 14 residues within 4Å: Chain C: W.33, D.46, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, H.139, E.421, F.422 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:W.33, C:A.53, C:W.56, C:R.57, C:V.60, C:F.104, C:F.104, C:H.139 Hydrogen bonds: C:S.103, C:F.422 Salt bridges: C:D.46 pi-Stacking: C:W.56, C:W.56, C:W.56 RNJ.25: 14 residues within 4Å: Chain D: W.33, D.46, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, H.139, E.421, F.422 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:W.33, D:A.53, D:W.56, D:R.57, D:V.60, D:F.104, D:F.104, D:H.139 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 RNJ.33: 14 residues within 4Å: Chain E: W.33, D.46, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, H.139, E.421, F.422 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:W.33, E:A.53, E:W.56, E:R.57, E:V.60, E:F.104, E:F.104, E:H.139 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 RNJ.41: 14 residues within 4Å: Chain F: W.33, D.46, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, H.139, E.421, F.422 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:W.33, F:A.53, F:W.56, F:R.57, F:V.60, F:F.104, F:F.104, F:H.139 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 PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 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: DMS.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.288, A:T.289, A:H.290 PEG.7: 7 residues within 4Å: Chain A: P.92, G.93, E.94, S.412, D.413, V.414 Ligands: DMS.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.93, A:S.412 PEG.10: 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: DMS.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.288, B:T.289, B:H.290 PEG.15: 7 residues within 4Å: Chain B: P.92, G.93, E.94, S.412, D.413, V.414 Ligands: DMS.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.93, B:S.412 PEG.18: 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: DMS.21 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.288, C:T.289, C:H.290 PEG.23: 7 residues within 4Å: Chain C: P.92, G.93, E.94, S.412, D.413, V.414 Ligands: DMS.22 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.93, C:S.412 PEG.26: 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: DMS.29 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.288, D:H.290 PEG.31: 7 residues within 4Å: Chain D: P.92, G.93, E.94, S.412, D.413, V.414 Ligands: DMS.30 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.93, D:S.412 PEG.34: 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: DMS.37 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:I.288, E:H.290 PEG.39: 7 residues within 4Å: Chain E: P.92, G.93, E.94, S.412, D.413, V.414 Ligands: DMS.38 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.93, E:S.412 PEG.42: 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: DMS.45 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:I.288, F:H.290 PEG.47: 7 residues within 4Å: Chain F: P.92, G.93, E.94, S.412, D.413, V.414 Ligands: DMS.46 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:G.93, F:S.412

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: P.61, Y.84, S.131, Y.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.84, A:Y.133, A:Y.133 GOL.11: 4 residues within 4Å: Chain B: P.61, Y.84, S.131, Y.133 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.84, B:Y.133, B:Y.133 GOL.19: 4 residues within 4Å: Chain C: P.61, Y.84, S.131, Y.133 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.84, C:Y.133, C:Y.133 GOL.27: 4 residues within 4Å: Chain D: P.61, Y.84, S.131, Y.133 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.133 GOL.35: 4 residues within 4Å: Chain E: P.61, Y.84, S.131, Y.133 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.133 GOL.43: 4 residues within 4Å: Chain F: P.61, Y.84, S.131, Y.133 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Y.133

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

DMS.4: 4 residues within 4Å: Chain A: W.33, R.57, V.60, T.62 Ligand excluded by PLIP DMS.5: 7 residues within 4Å: Chain A: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.2 Ligand excluded by PLIP DMS.6: 7 residues within 4Å: Chain A: P.92, G.329, Y.330, A.411, S.412, D.413 Ligands: PEG.7 Ligand excluded by PLIP DMS.8: 2 residues within 4Å: Chain A: E.159, W.309 Ligand excluded by PLIP DMS.12: 4 residues within 4Å: Chain B: W.33, R.57, V.60, T.62 Ligand excluded by PLIP DMS.13: 7 residues within 4Å: Chain B: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.10 Ligand excluded by PLIP DMS.14: 7 residues within 4Å: Chain B: P.92, G.329, Y.330, A.411, S.412, D.413 Ligands: PEG.15 Ligand excluded by PLIP DMS.16: 2 residues within 4Å: Chain B: E.159, W.309 Ligand excluded by PLIP DMS.20: 4 residues within 4Å: Chain C: W.33, R.57, V.60, T.62 Ligand excluded by PLIP DMS.21: 7 residues within 4Å: Chain C: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.18 Ligand excluded by PLIP DMS.22: 7 residues within 4Å: Chain C: P.92, G.329, Y.330, A.411, S.412, D.413 Ligands: PEG.23 Ligand excluded by PLIP DMS.24: 2 residues within 4Å: Chain C: E.159, W.309 Ligand excluded by PLIP DMS.28: 4 residues within 4Å: Chain D: W.33, R.57, V.60, T.62 Ligand excluded by PLIP DMS.29: 7 residues within 4Å: Chain D: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.26 Ligand excluded by PLIP DMS.30: 7 residues within 4Å: Chain D: P.92, G.329, Y.330, A.411, S.412, D.413 Ligands: PEG.31 Ligand excluded by PLIP DMS.32: 2 residues within 4Å: Chain D: E.159, W.309 Ligand excluded by PLIP DMS.36: 4 residues within 4Å: Chain E: W.33, R.57, V.60, T.62 Ligand excluded by PLIP DMS.37: 7 residues within 4Å: Chain E: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.34 Ligand excluded by PLIP DMS.38: 7 residues within 4Å: Chain E: P.92, G.329, Y.330, A.411, S.412, D.413 Ligands: PEG.39 Ligand excluded by PLIP DMS.40: 2 residues within 4Å: Chain E: E.159, W.309 Ligand excluded by PLIP DMS.44: 4 residues within 4Å: Chain F: W.33, R.57, V.60, T.62 Ligand excluded by PLIP DMS.45: 7 residues within 4Å: Chain F: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.42 Ligand excluded by PLIP DMS.46: 7 residues within 4Å: Chain F: P.92, G.329, Y.330, A.411, S.412, D.413 Ligands: PEG.47 Ligand excluded by PLIP DMS.48: 2 residues within 4Å: Chain F: E.159, W.309 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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