SMTL ID : 6vv3.1

Crystal structure of Eis from Mycobacterium tuberculosis in complex with inhibitor SGT1358

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

6 x RM7: 2-[(4-amino-6,7,8,9-tetrahydro-5H-cyclohepta[4,5]thieno[2,3-d]pyrimidin-2-yl)sulfanyl]-N-[2-(piperidin-1-yl)ethyl]acetamide(Non-covalent)

RM7.1: 15 residues within 4Å: Chain A: W.33, F.44, D.46, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: PEG.4 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.33, A:F.44, A:A.53, A:W.56, A:W.56, A:R.57, A:V.60, A:L.83, A:F.104, A:F.104 Hydrogen bonds: A:S.103, A:F.422, A:F.422 Salt bridges: A:D.46 pi-Stacking: A:W.56, A:W.56 RM7.8: 15 residues within 4Å: Chain B: W.33, F.44, D.46, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: PEG.11 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.33, B:F.44, B:A.53, B:W.56, B:W.56, B:R.57, B:V.60, B:L.83, B:F.104, B:F.104 Hydrogen bonds: B:S.103, B:F.422, B:F.422 Salt bridges: B:D.46 pi-Stacking: B:W.56, B:W.56 RM7.15: 15 residues within 4Å: Chain C: W.33, F.44, D.46, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: PEG.18 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:W.33, C:F.44, C:A.53, C:W.56, C:W.56, C:R.57, C:V.60, C:L.83, C:F.104, C:F.104 Hydrogen bonds: C:S.103, C:F.422, C:F.422 Salt bridges: C:D.46 pi-Stacking: C:W.56, C:W.56 RM7.22: 15 residues within 4Å: Chain D: W.33, F.44, D.46, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: PEG.25 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:W.33, D:F.44, D:A.53, D:W.56, D:W.56, D:R.57, D:V.60, D:L.83, D:F.104, D:F.104 Hydrogen bonds: D:S.103, D:F.422, D:F.422, D:F.422 Water bridges: D:E.421 Salt bridges: D:D.46 pi-Stacking: D:W.56, D:W.56 RM7.29: 15 residues within 4Å: Chain E: W.33, F.44, D.46, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: PEG.32 18 PLIP interactions: 18 interactions with chain E Hydrophobic interactions: E:W.33, E:F.44, E:A.53, E:W.56, E:W.56, E:R.57, E:V.60, E:L.83, E:F.104, E:F.104 Hydrogen bonds: E:S.103, E:F.422, E:F.422, E:F.422 Water bridges: E:E.421 Salt bridges: E:D.46 pi-Stacking: E:W.56, E:W.56 RM7.36: 15 residues within 4Å: Chain F: W.33, F.44, D.46, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: PEG.39 18 PLIP interactions: 18 interactions with chain F Hydrophobic interactions: F:W.33, F:F.44, F:A.53, F:W.56, F:W.56, F:R.57, F:V.60, F:L.83, F:F.104, F:F.104 Hydrogen bonds: F:S.103, F:F.422, F:F.422, F:F.422 Water bridges: F:E.421 Salt bridges: F:D.46 pi-Stacking: F:W.56, F:W.56

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

DMS.2: 6 residues within 4Å: Chain A: A.367, E.368, E.370, R.396, T.397, K.398 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.370 Salt bridges: A:E.370 DMS.9: 6 residues within 4Å: Chain B: A.367, E.368, E.370, R.396, T.397, K.398 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.370 Salt bridges: B:E.370 DMS.16: 6 residues within 4Å: Chain C: A.367, E.368, E.370, R.396, T.397, K.398 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.370 Salt bridges: C:E.370 DMS.23: 6 residues within 4Å: Chain D: A.367, E.368, E.370, R.396, T.397, K.398 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:E.370 DMS.30: 6 residues within 4Å: Chain E: A.367, E.368, E.370, R.396, T.397, K.398 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:E.370 DMS.37: 6 residues within 4Å: Chain F: A.367, E.368, E.370, R.396, T.397, K.398 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:E.370

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

PEG.3: 5 residues within 4Å: Chain A: A.197, E.200, R.212, P.213, Q.214 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.212, A:Q.214 Water bridges: A:A.197, A:E.200, A:E.200, A:R.201 PEG.4: 9 residues within 4Å: Chain A: I.48, S.52, W.56, R.212, L.216, E.219, L.220, E.223 Ligands: RM7.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.52, A:S.52, A:R.212, A:E.219 PEG.10: 5 residues within 4Å: Chain B: A.197, E.200, R.212, P.213, Q.214 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.212, B:Q.214 Water bridges: B:A.197, B:E.200, B:E.200, B:R.201 PEG.11: 9 residues within 4Å: Chain B: I.48, S.52, W.56, R.212, L.216, E.219, L.220, E.223 Ligands: RM7.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.52, B:S.52, B:R.212, B:E.219 PEG.17: 5 residues within 4Å: Chain C: A.197, E.200, R.212, P.213, Q.214 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.212, C:Q.214 Water bridges: C:A.197, C:E.200, C:E.200, C:R.201 PEG.18: 9 residues within 4Å: Chain C: I.48, S.52, W.56, R.212, L.216, E.219, L.220, E.223 Ligands: RM7.15 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.52, C:S.52, C:R.212, C:E.219 PEG.24: 5 residues within 4Å: Chain D: A.197, E.200, R.212, P.213, Q.214 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.212, D:Q.214 Water bridges: D:A.197, D:E.200, D:R.201 PEG.25: 9 residues within 4Å: Chain D: I.48, S.52, W.56, R.212, L.216, E.219, L.220, E.223 Ligands: RM7.22 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.52, D:S.52, D:R.212 PEG.31: 5 residues within 4Å: Chain E: A.197, E.200, R.212, P.213, Q.214 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:R.212, E:Q.214 Water bridges: E:A.197, E:E.200, E:R.201 PEG.32: 9 residues within 4Å: Chain E: I.48, S.52, W.56, R.212, L.216, E.219, L.220, E.223 Ligands: RM7.29 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.52, E:S.52, E:R.212 PEG.38: 5 residues within 4Å: Chain F: A.197, E.200, R.212, P.213, Q.214 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:R.212, F:Q.214 Water bridges: F:A.197, F:E.200, F:R.201 PEG.39: 9 residues within 4Å: Chain F: I.48, S.52, W.56, R.212, L.216, E.219, L.220, E.223 Ligands: RM7.36 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.52, F:S.52, F:R.212

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

SO4.5: 8 residues within 4Å: Chain A: P.92, G.93, G.329, Y.330, A.331, A.411, S.412, D.413 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.93, A:A.411, A:D.413 SO4.12: 8 residues within 4Å: Chain B: P.92, G.93, G.329, Y.330, A.331, A.411, S.412, D.413 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.93, B:A.411, B:D.413 SO4.19: 8 residues within 4Å: Chain C: P.92, G.93, G.329, Y.330, A.331, A.411, S.412, D.413 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.93, C:A.411, C:D.413 SO4.26: 8 residues within 4Å: Chain D: P.92, G.93, G.329, Y.330, A.331, A.411, S.412, D.413 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.93, D:A.411, D:D.413 Water bridges: D:H.332 SO4.33: 8 residues within 4Å: Chain E: P.92, G.93, G.329, Y.330, A.331, A.411, S.412, D.413 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.93, E:A.411, E:D.413 Water bridges: E:H.332 SO4.40: 8 residues within 4Å: Chain F: P.92, G.93, G.329, Y.330, A.331, A.411, S.412, D.413 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:G.93, F:A.411, F:D.413 Water bridges: F:H.332

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

CL.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.20: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.28: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.34: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.35: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.41: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.42: 0 residues within 4Å: (No contacts) 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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