SMTL ID : 6vuz.1

Crystal structure of Eis from Mycobacterium tuberculosis in complex with inhibitor SGT353

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-hexamer

Ligands

6 x RMS: 2-{[3-(piperidin-1-yl)propyl]sulfanyl}-6,7-dihydro-5H-cyclopenta[4,5]thieno[2,3-d]pyrimidin-4-amine(Non-covalent)

RMS.1: 14 residues within 4Å: Chain A: D.46, I.48, A.53, W.56, R.57, L.83, M.85, S.103, F.104, H.139, A.140, E.421, F.422 Ligands: SO4.6 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.56, A:L.83, A:L.83, A:F.104, A:F.104 Hydrogen bonds: A:S.103, A:F.422 Salt bridges: A:D.46, A:E.421 pi-Stacking: A:W.56, A:W.56, A:W.56 RMS.7: 14 residues within 4Å: Chain B: D.46, I.48, A.53, W.56, R.57, L.83, M.85, S.103, F.104, H.139, A.140, E.421, F.422 Ligands: SO4.12 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.56, B:L.83, B:L.83, B:F.104, B:F.104 Hydrogen bonds: B:S.103, B:F.422 Salt bridges: B:D.46, B:E.421 pi-Stacking: B:W.56, B:W.56, B:W.56 RMS.13: 14 residues within 4Å: Chain C: D.46, I.48, A.53, W.56, R.57, L.83, M.85, S.103, F.104, H.139, A.140, E.421, F.422 Ligands: SO4.18 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:W.56, C:L.83, C:L.83, C:F.104, C:F.104 Hydrogen bonds: C:S.103, C:F.422 Salt bridges: C:D.46, C:E.421 pi-Stacking: C:W.56, C:W.56, C:W.56 RMS.19: 14 residues within 4Å: Chain D: D.46, I.48, A.53, W.56, R.57, L.83, M.85, S.103, F.104, H.139, A.140, E.421, F.422 Ligands: SO4.24 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:W.56, D:L.83, D:L.83, D:F.104, D:F.104 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, D:W.56 RMS.25: 14 residues within 4Å: Chain E: D.46, I.48, A.53, W.56, R.57, L.83, M.85, S.103, F.104, H.139, A.140, E.421, F.422 Ligands: SO4.30 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:W.56, E:L.83, E:L.83, E:F.104, E:F.104 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, E:W.56 RMS.31: 14 residues within 4Å: Chain F: D.46, I.48, A.53, W.56, R.57, L.83, M.85, S.103, F.104, H.139, A.140, E.421, F.422 Ligands: SO4.36 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:W.56, F:L.83, F:L.83, F:F.104, F:F.104 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, F:W.56

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

PEG.2: 5 residues within 4Å: Chain A: P.61, Y.84, D.86, S.131, Y.133 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.84, A:D.86, A:S.131, A:S.131, A:Y.133 PEG.5: 9 residues within 4Å: Chain A: L.261, H.269, I.287, I.288, T.289, H.290, D.293, P.294, Q.417 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.288, A:T.289 Water bridges: A:L.261, A:Q.417 PEG.8: 5 residues within 4Å: Chain B: P.61, Y.84, D.86, S.131, Y.133 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.84, B:D.86, B:S.131, B:S.131, B:Y.133 PEG.11: 9 residues within 4Å: Chain B: L.261, H.269, I.287, I.288, T.289, H.290, D.293, P.294, Q.417 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.288, B:T.289 Water bridges: B:L.261, B:Q.417 PEG.14: 5 residues within 4Å: Chain C: P.61, Y.84, D.86, S.131, Y.133 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.84, C:D.86, C:S.131, C:S.131, C:Y.133 PEG.17: 9 residues within 4Å: Chain C: L.261, H.269, I.287, I.288, T.289, H.290, D.293, P.294, Q.417 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:I.288, C:T.289 Water bridges: C:L.261, C:Q.417 PEG.20: 5 residues within 4Å: Chain D: P.61, Y.84, D.86, S.131, Y.133 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.131, D:S.131 PEG.23: 9 residues within 4Å: Chain D: L.261, H.269, I.287, I.288, T.289, H.290, D.293, P.294, Q.417 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:I.288 Water bridges: D:L.261, D:Q.417 PEG.26: 5 residues within 4Å: Chain E: P.61, Y.84, D.86, S.131, Y.133 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.131, E:S.131 PEG.29: 9 residues within 4Å: Chain E: L.261, H.269, I.287, I.288, T.289, H.290, D.293, P.294, Q.417 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:I.288 Water bridges: E:L.261, E:Q.417 PEG.32: 5 residues within 4Å: Chain F: P.61, Y.84, D.86, S.131, Y.133 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:S.131, F:S.131 PEG.35: 9 residues within 4Å: Chain F: L.261, H.269, I.287, I.288, T.289, H.290, D.293, P.294, Q.417 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:I.288 Water bridges: F:L.261, F:Q.417

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: R.112, R.113, R.114, G.115, L.116, L.117, R.118 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.112, A:R.114, A:G.115, A:L.116, A:L.117, A:R.118 GOL.9: 7 residues within 4Å: Chain B: R.112, R.113, R.114, G.115, L.116, L.117, R.118 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.112, B:R.114, B:G.115, B:L.116, B:L.117, B:R.118 GOL.15: 7 residues within 4Å: Chain C: R.112, R.113, R.114, G.115, L.116, L.117, R.118 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.112, C:R.114, C:G.115, C:L.116, C:L.117, C:R.118 GOL.21: 7 residues within 4Å: Chain D: R.112, R.113, R.114, G.115, L.116, L.117, R.118 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.112, D:R.114, D:G.115, D:L.116, D:L.117, D:R.118 GOL.27: 7 residues within 4Å: Chain E: R.112, R.113, R.114, G.115, L.116, L.117, R.118 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:R.112, E:R.114, E:G.115, E:L.116, E:L.117, E:R.118 GOL.33: 7 residues within 4Å: Chain F: R.112, R.113, R.114, G.115, L.116, L.117, R.118 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:R.112, F:R.114, F:G.115, F:L.116, F:L.117, F:R.118

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

SO4.4: 9 residues within 4Å: Chain A: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, S.412, D.413 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.93, A:R.328, A:G.329, A:D.413 SO4.6: 4 residues within 4Å: Chain A: F.44, D.46, F.422 Ligands: RMS.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.46, A:F.104 SO4.10: 9 residues within 4Å: Chain B: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, S.412, D.413 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.93, B:R.328, B:G.329, B:D.413 SO4.12: 4 residues within 4Å: Chain B: F.44, D.46, F.422 Ligands: RMS.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.46, B:F.104 SO4.16: 9 residues within 4Å: Chain C: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, S.412, D.413 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.93, C:R.328, C:G.329, C:D.413 SO4.18: 4 residues within 4Å: Chain C: F.44, D.46, F.422 Ligands: RMS.13 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.46, C:F.104 SO4.22: 9 residues within 4Å: Chain D: P.92, G.93, R.328, 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:R.328, D:G.329, D:D.413 SO4.24: 4 residues within 4Å: Chain D: F.44, D.46, F.422 Ligands: RMS.19 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.46, D:F.104 SO4.28: 9 residues within 4Å: Chain E: P.92, G.93, R.328, 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:R.328, E:G.329, E:D.413 SO4.30: 4 residues within 4Å: Chain E: F.44, D.46, F.422 Ligands: RMS.25 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.46, E:F.104 SO4.34: 9 residues within 4Å: Chain F: P.92, G.93, R.328, 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:R.328, F:G.329, F:D.413 SO4.36: 4 residues within 4Å: Chain F: F.44, D.46, F.422 Ligands: RMS.31 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.46, F:F.104

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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