SMTL ID : 6vv2.1

Crystal structure of Eis from Mycobacterium tuberculosis in complex with inhibitor SGT1348

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-hexamer

Ligands

6 x RMG: 2-{[3-(piperidin-1-yl)propyl]sulfanyl}-6,7,8,9-tetrahydro-5H-cyclohepta[4,5]thieno[2,3-d]pyrimidin-4-amine(Non-covalent)

RMG.1: 13 residues within 4Å: Chain A: W.33, D.46, 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 A Hydrophobic interactions: A:W.33, A:A.53, A:W.56, A:R.57, A:V.60, A:L.83, A:F.104, A:F.104, A:H.139 Hydrogen bonds: A:S.103, A:F.422 Salt bridges: A:D.46, A:E.421 pi-Stacking: A:W.56, A:W.56 RMG.8: 13 residues within 4Å: Chain B: W.33, D.46, 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 B Hydrophobic interactions: B:W.33, B:A.53, B:W.56, B:R.57, B:V.60, B:L.83, B:F.104, B:F.104, B:H.139 Hydrogen bonds: B:S.103, B:F.422 Salt bridges: B:D.46, B:E.421 pi-Stacking: B:W.56, B:W.56 RMG.15: 13 residues within 4Å: Chain C: W.33, D.46, 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 C Hydrophobic interactions: C:W.33, C:A.53, C:W.56, C:R.57, C:V.60, C:L.83, C:F.104, C:F.104, C:H.139 Hydrogen bonds: C:S.103, C:F.422 Salt bridges: C:D.46, C:E.421 pi-Stacking: C:W.56, C:W.56 RMG.22: 13 residues within 4Å: Chain D: W.33, D.46, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, H.139, E.421, F.422 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:W.33, D:A.53, D:W.56, D:R.57, D:V.60, D:L.83, 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, D:E.421 pi-Stacking: D:W.56, D:W.56 RMG.29: 13 residues within 4Å: Chain E: W.33, D.46, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, H.139, E.421, F.422 16 PLIP interactions: 16 interactions with chain E Hydrophobic interactions: E:W.33, E:A.53, E:W.56, E:R.57, E:V.60, E:L.83, 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, E:E.421 pi-Stacking: E:W.56, E:W.56 RMG.36: 13 residues within 4Å: Chain F: W.33, D.46, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, H.139, E.421, F.422 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:W.33, F:A.53, F:W.56, F:R.57, F:V.60, F:L.83, 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, F:E.421 pi-Stacking: F:W.56, F:W.56

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

PEG.2: 5 residues within 4Å: Chain A: E.196, A.197, E.200, R.212, Q.214 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.212, A:Q.214 Water bridges: A:E.200 PEG.9: 5 residues within 4Å: Chain B: E.196, A.197, E.200, R.212, Q.214 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.212, B:Q.214 Water bridges: B:E.200 PEG.16: 5 residues within 4Å: Chain C: E.196, A.197, E.200, R.212, Q.214 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.212, C:Q.214 Water bridges: C:E.200 PEG.23: 5 residues within 4Å: Chain D: E.196, A.197, E.200, R.212, Q.214 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.212, D:Q.214 PEG.30: 5 residues within 4Å: Chain E: E.196, A.197, E.200, R.212, Q.214 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.212, E:Q.214 PEG.37: 5 residues within 4Å: Chain F: E.196, A.197, E.200, R.212, Q.214 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.212, F:Q.214

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: H.125, R.126, A.129, R.317, M.319, R.373 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.125, A:R.317, A:R.317, A:M.319 GOL.10: 6 residues within 4Å: Chain B: H.125, R.126, A.129, R.317, M.319, R.373 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.125, B:R.317, B:R.317, B:M.319 GOL.17: 6 residues within 4Å: Chain C: H.125, R.126, A.129, R.317, M.319, R.373 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.125, C:R.317, C:R.317, C:M.319 GOL.24: 6 residues within 4Å: Chain D: H.125, R.126, A.129, R.317, M.319, R.373 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.125, D:R.317, D:R.317, D:M.319 GOL.31: 6 residues within 4Å: Chain E: H.125, R.126, A.129, R.317, M.319, R.373 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:H.125, E:R.317, E:R.317, E:M.319 GOL.38: 6 residues within 4Å: Chain F: H.125, R.126, A.129, R.317, M.319, R.373 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:H.125, F:R.317, F:R.317, F:M.319

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

SO4.4: 6 residues within 4Å: Chain A: W.33, R.57, V.60, P.61, T.62, A.65 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.57, A:V.60 Water bridges: A:D.63, A:A.65, A:A.65 SO4.11: 6 residues within 4Å: Chain B: W.33, R.57, V.60, P.61, T.62, A.65 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.57, B:V.60 Water bridges: B:D.63, B:A.65, B:A.65 SO4.18: 6 residues within 4Å: Chain C: W.33, R.57, V.60, P.61, T.62, A.65 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.57, C:V.60 Water bridges: C:D.63, C:A.65, C:A.65 SO4.25: 6 residues within 4Å: Chain D: W.33, R.57, V.60, P.61, T.62, A.65 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.57, D:V.60 Water bridges: D:D.63, D:A.65, D:A.65 SO4.32: 6 residues within 4Å: Chain E: W.33, R.57, V.60, P.61, T.62, A.65 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:R.57, E:V.60 Water bridges: E:D.63, E:A.65, E:A.65 SO4.39: 6 residues within 4Å: Chain F: W.33, R.57, V.60, P.61, T.62, A.65 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:R.57, F:V.60 Water bridges: F:D.63, F:A.65, F:A.65

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

DMS.5: 7 residues within 4Å: Chain A: G.93, R.328, Y.330, A.331, A.411, S.412, D.413 No protein-ligand interaction detected (PLIP) DMS.12: 7 residues within 4Å: Chain B: G.93, R.328, Y.330, A.331, A.411, S.412, D.413 No protein-ligand interaction detected (PLIP) DMS.19: 7 residues within 4Å: Chain C: G.93, R.328, Y.330, A.331, A.411, S.412, D.413 No protein-ligand interaction detected (PLIP) DMS.26: 7 residues within 4Å: Chain D: G.93, R.328, Y.330, A.331, A.411, S.412, D.413 No protein-ligand interaction detected (PLIP) DMS.33: 7 residues within 4Å: Chain E: G.93, R.328, Y.330, A.331, A.411, S.412, D.413 No protein-ligand interaction detected (PLIP) DMS.40: 7 residues within 4Å: Chain F: G.93, R.328, Y.330, A.331, A.411, S.412, D.413 No protein-ligand interaction detected (PLIP)

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

NA.6: 7 residues within 4Å: Chain A: A.392, R.394 Chain E: H.170, D.172, A.173, H.297, L.298 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:H.297 NA.13: 7 residues within 4Å: Chain B: A.392, R.394 Chain D: H.170, D.172, A.173, H.297, L.298 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.392 NA.20: 7 residues within 4Å: Chain C: A.392, R.394 Chain F: H.170, D.172, A.173, H.297, L.298 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.392 NA.27: 7 residues within 4Å: Chain B: H.170, D.172, A.173, H.297, L.298 Chain D: A.392, R.394 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.297 NA.34: 7 residues within 4Å: Chain A: H.170, D.172, A.173, H.297, L.298 Chain E: A.392, R.394 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.297 NA.41: 7 residues within 4Å: Chain C: H.170, D.172, A.173, H.297, L.298 Chain F: A.392, R.394 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.297

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

CL.7: 2 residues within 4Å: Chain A: T.289, T.418 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: T.289, T.418 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain C: T.289, T.418 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain D: T.289, T.418 Ligand excluded by PLIP CL.35: 2 residues within 4Å: Chain E: T.289, T.418 Ligand excluded by PLIP CL.42: 2 residues within 4Å: Chain F: T.289, T.418 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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