SMTL ID : 6vv0.1

Crystal structure of Eis from Mycobacterium tuberculosis in complex with inhibitor SGT1354

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-hexamer

Ligands

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

RMV.1: 11 residues within 4Å: Chain A: F.44, D.46, I.48, 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 RMV.9: 11 residues within 4Å: Chain B: F.44, D.46, I.48, 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 RMV.17: 11 residues within 4Å: Chain C: F.44, D.46, I.48, 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 RMV.25: 11 residues within 4Å: Chain D: F.44, D.46, I.48, A.53, W.56, L.83, M.85, S.103, F.104, E.421, F.422 14 PLIP interactions: 14 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:E.421, D:F.422, D:F.422 Salt bridges: D:D.46 pi-Stacking: D:W.56, D:W.56 RMV.33: 11 residues within 4Å: Chain E: F.44, D.46, I.48, A.53, W.56, L.83, M.85, S.103, F.104, E.421, F.422 14 PLIP interactions: 14 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:E.421, E:F.422, E:F.422 Salt bridges: E:D.46 pi-Stacking: E:W.56, E:W.56 RMV.41: 11 residues within 4Å: Chain F: F.44, D.46, I.48, A.53, W.56, L.83, M.85, S.103, F.104, E.421, F.422 14 PLIP interactions: 14 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:E.421, F:F.422, F:F.422 Salt bridges: F:D.46 pi-Stacking: F:W.56, F:W.56

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

PEG.2: 4 residues within 4Å: Chain A: W.202, L.261, A.263, Q.417 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.263, A:T.289, A:D.293, A:Q.417 PEG.3: 6 residues within 4Å: Chain A: P.92, G.93, E.94, P.207, V.414 Ligands: DMS.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.93, A:G.93, A:E.94 PEG.10: 4 residues within 4Å: Chain B: W.202, L.261, A.263, Q.417 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.263, B:T.289, B:D.293, B:Q.417 PEG.11: 6 residues within 4Å: Chain B: P.92, G.93, E.94, P.207, V.414 Ligands: DMS.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.93, B:G.93, B:E.94 PEG.18: 4 residues within 4Å: Chain C: W.202, L.261, A.263, Q.417 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.263, C:T.289, C:D.293, C:Q.417 PEG.19: 6 residues within 4Å: Chain C: P.92, G.93, E.94, P.207, V.414 Ligands: DMS.20 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.93, C:G.93, C:E.94 PEG.26: 4 residues within 4Å: Chain D: W.202, L.261, A.263, Q.417 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.263, D:D.293, D:Q.417 PEG.27: 6 residues within 4Å: Chain D: P.92, G.93, E.94, P.207, V.414 Ligands: DMS.28 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.93, D:G.93, D:E.94 PEG.34: 4 residues within 4Å: Chain E: W.202, L.261, A.263, Q.417 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:A.263, E:D.293, E:Q.417 PEG.35: 6 residues within 4Å: Chain E: P.92, G.93, E.94, P.207, V.414 Ligands: DMS.36 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.93, E:G.93, E:E.94 PEG.42: 4 residues within 4Å: Chain F: W.202, L.261, A.263, Q.417 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:A.263, F:D.293, F:Q.417 PEG.43: 6 residues within 4Å: Chain F: P.92, G.93, E.94, P.207, V.414 Ligands: DMS.44 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:G.93, F:G.93, F:E.94

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

DMS.4: 9 residues within 4Å: Chain A: G.93, R.328, G.329, Y.330, A.331, A.411, S.412, D.413 Ligands: PEG.3 Ligand excluded by PLIP DMS.5: 6 residues within 4Å: Chain A: P.28, W.33, R.57, P.61, T.62, D.63 Ligand excluded by PLIP DMS.8: 6 residues within 4Å: Chain A: R.262, I.288, T.289, H.290, Q.417, T.418 Ligand excluded by PLIP DMS.12: 9 residues within 4Å: Chain B: G.93, R.328, G.329, Y.330, A.331, A.411, S.412, D.413 Ligands: PEG.11 Ligand excluded by PLIP DMS.13: 6 residues within 4Å: Chain B: P.28, W.33, R.57, P.61, T.62, D.63 Ligand excluded by PLIP DMS.16: 6 residues within 4Å: Chain B: R.262, I.288, T.289, H.290, Q.417, T.418 Ligand excluded by PLIP DMS.20: 9 residues within 4Å: Chain C: G.93, R.328, G.329, Y.330, A.331, A.411, S.412, D.413 Ligands: PEG.19 Ligand excluded by PLIP DMS.21: 6 residues within 4Å: Chain C: P.28, W.33, R.57, P.61, T.62, D.63 Ligand excluded by PLIP DMS.24: 6 residues within 4Å: Chain C: R.262, I.288, T.289, H.290, Q.417, T.418 Ligand excluded by PLIP DMS.28: 9 residues within 4Å: Chain D: G.93, R.328, G.329, Y.330, A.331, A.411, S.412, D.413 Ligands: PEG.27 Ligand excluded by PLIP DMS.29: 6 residues within 4Å: Chain D: P.28, W.33, R.57, P.61, T.62, D.63 Ligand excluded by PLIP DMS.32: 6 residues within 4Å: Chain D: R.262, I.288, T.289, H.290, Q.417, T.418 Ligand excluded by PLIP DMS.36: 9 residues within 4Å: Chain E: G.93, R.328, G.329, Y.330, A.331, A.411, S.412, D.413 Ligands: PEG.35 Ligand excluded by PLIP DMS.37: 6 residues within 4Å: Chain E: P.28, W.33, R.57, P.61, T.62, D.63 Ligand excluded by PLIP DMS.40: 6 residues within 4Å: Chain E: R.262, I.288, T.289, H.290, Q.417, T.418 Ligand excluded by PLIP DMS.44: 9 residues within 4Å: Chain F: G.93, R.328, G.329, Y.330, A.331, A.411, S.412, D.413 Ligands: PEG.43 Ligand excluded by PLIP DMS.45: 6 residues within 4Å: Chain F: P.28, W.33, R.57, P.61, T.62, D.63 Ligand excluded by PLIP DMS.48: 6 residues within 4Å: Chain F: R.262, I.288, T.289, H.290, Q.417, T.418 Ligand excluded by PLIP

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

SO4.6: 3 residues within 4Å: Chain A: E.159, I.288, W.309 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.159 SO4.14: 3 residues within 4Å: Chain B: E.159, I.288, W.309 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.159 SO4.22: 3 residues within 4Å: Chain C: E.159, I.288, W.309 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.159 SO4.30: 3 residues within 4Å: Chain D: E.159, I.288, W.309 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.159 SO4.38: 3 residues within 4Å: Chain E: E.159, I.288, W.309 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.159 SO4.46: 3 residues within 4Å: Chain F: E.159, I.288, W.309 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.159

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: H.125, R.126, R.317, M.319 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.125, A:R.317, A:R.317, A:M.319 GOL.15: 4 residues within 4Å: Chain B: H.125, R.126, R.317, M.319 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.125, B:R.317, B:R.317, B:M.319 GOL.23: 4 residues within 4Å: Chain C: H.125, R.126, R.317, M.319 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.125, C:R.317, C:R.317, C:M.319 GOL.31: 4 residues within 4Å: Chain D: H.125, R.126, R.317, M.319 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.125, D:R.317, D:R.317, D:M.319 GOL.39: 4 residues within 4Å: Chain E: H.125, R.126, R.317, M.319 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:H.125, E:R.317, E:R.317, E:M.319 GOL.47: 4 residues within 4Å: Chain F: H.125, R.126, R.317, M.319 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:H.125, F:R.317, F:R.317, F:M.319

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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