SMTL ID : 8f55.1

Crystal structure of acetyltransferase Eis from Mycobacterium tuberculosis H37Rv in complex with inhibitor SGT1614

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

6 x XF2: (2E)-2-[(4-chlorophenyl)methylidene]hydrazine-1-carboximidamide(Non-covalent)

XF2.1: 12 residues within 4Å: Chain A: W.33, I.48, A.53, W.56, R.57, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: DMS.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.56, A:L.83, A:F.104 Hydrogen bonds: A:W.56, A:S.103, A:F.422 pi-Cation interactions: A:W.56 XF2.13: 12 residues within 4Å: Chain B: W.33, I.48, A.53, W.56, R.57, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: DMS.14 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.56, B:L.83, B:F.104 Hydrogen bonds: B:W.56, B:S.103, B:F.422 pi-Cation interactions: B:W.56 XF2.25: 12 residues within 4Å: Chain C: W.33, I.48, A.53, W.56, R.57, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: DMS.26 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:W.56, C:L.83, C:F.104 Hydrogen bonds: C:W.56, C:S.103, C:F.422 pi-Cation interactions: C:W.56 XF2.37: 12 residues within 4Å: Chain D: W.33, I.48, A.53, W.56, R.57, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: DMS.38 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:W.56, D:L.83, D:F.104 Hydrogen bonds: D:W.56, D:S.103, D:F.422, D:F.422 pi-Cation interactions: D:W.56 XF2.49: 12 residues within 4Å: Chain E: W.33, I.48, A.53, W.56, R.57, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: DMS.50 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:W.56, E:L.83, E:F.104 Hydrogen bonds: E:W.56, E:S.103, E:F.422, E:F.422 pi-Cation interactions: E:W.56 XF2.61: 12 residues within 4Å: Chain F: W.33, I.48, A.53, W.56, R.57, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: DMS.62 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:W.56, F:L.83, F:F.104 Hydrogen bonds: F:W.56, F:S.103, F:F.422, F:F.422 pi-Cation interactions: F:W.56

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

DMS.2: 5 residues within 4Å: Chain A: F.44, D.46, F.47, I.48 Ligands: XF2.1 Ligand excluded by PLIP DMS.3: 3 residues within 4Å: Chain A: E.159, R.257 Ligands: DMS.7 Ligand excluded by PLIP DMS.4: 8 residues within 4Å: Chain A: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: GOL.6, PEG.12 Ligand excluded by PLIP DMS.5: 8 residues within 4Å: Chain A: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, D.413 Ligand excluded by PLIP DMS.7: 4 residues within 4Å: Chain A: W.309, E.421 Ligands: DMS.3, GOL.6 Ligand excluded by PLIP DMS.8: 5 residues within 4Å: Chain A: P.28, W.33, R.57, P.61, A.65 Ligand excluded by PLIP DMS.9: 5 residues within 4Å: Chain A: A.367, E.368, E.370, R.396, T.397 Ligand excluded by PLIP DMS.14: 5 residues within 4Å: Chain B: F.44, D.46, F.47, I.48 Ligands: XF2.13 Ligand excluded by PLIP DMS.15: 3 residues within 4Å: Chain B: E.159, R.257 Ligands: DMS.19 Ligand excluded by PLIP DMS.16: 8 residues within 4Å: Chain B: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: GOL.18, PEG.24 Ligand excluded by PLIP DMS.17: 8 residues within 4Å: Chain B: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, D.413 Ligand excluded by PLIP DMS.19: 4 residues within 4Å: Chain B: W.309, E.421 Ligands: DMS.15, GOL.18 Ligand excluded by PLIP DMS.20: 5 residues within 4Å: Chain B: P.28, W.33, R.57, P.61, A.65 Ligand excluded by PLIP DMS.21: 5 residues within 4Å: Chain B: A.367, E.368, E.370, R.396, T.397 Ligand excluded by PLIP DMS.26: 5 residues within 4Å: Chain C: F.44, D.46, F.47, I.48 Ligands: XF2.25 Ligand excluded by PLIP DMS.27: 3 residues within 4Å: Chain C: E.159, R.257 Ligands: DMS.31 Ligand excluded by PLIP DMS.28: 8 residues within 4Å: Chain C: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: GOL.30, PEG.36 Ligand excluded by PLIP DMS.29: 8 residues within 4Å: Chain C: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, D.413 Ligand excluded by PLIP DMS.31: 4 residues within 4Å: Chain C: W.309, E.421 Ligands: DMS.27, GOL.30 Ligand excluded by PLIP DMS.32: 5 residues within 4Å: Chain C: P.28, W.33, R.57, P.61, A.65 Ligand excluded by PLIP DMS.33: 5 residues within 4Å: Chain C: A.367, E.368, E.370, R.396, T.397 Ligand excluded by PLIP DMS.38: 5 residues within 4Å: Chain D: F.44, D.46, F.47, I.48 Ligands: XF2.37 Ligand excluded by PLIP DMS.39: 3 residues within 4Å: Chain D: E.159, R.257 Ligands: DMS.43 Ligand excluded by PLIP DMS.40: 8 residues within 4Å: Chain D: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: GOL.42, PEG.48 Ligand excluded by PLIP DMS.41: 8 residues within 4Å: Chain D: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, D.413 Ligand excluded by PLIP DMS.43: 4 residues within 4Å: Chain D: W.309, E.421 Ligands: DMS.39, GOL.42 Ligand excluded by PLIP DMS.44: 5 residues within 4Å: Chain D: P.28, W.33, R.57, P.61, A.65 Ligand excluded by PLIP DMS.45: 5 residues within 4Å: Chain D: A.367, E.368, E.370, R.396, T.397 Ligand excluded by PLIP DMS.50: 5 residues within 4Å: Chain E: F.44, D.46, F.47, I.48 Ligands: XF2.49 Ligand excluded by PLIP DMS.51: 3 residues within 4Å: Chain E: E.159, R.257 Ligands: DMS.55 Ligand excluded by PLIP DMS.52: 8 residues within 4Å: Chain E: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: GOL.54, PEG.60 Ligand excluded by PLIP DMS.53: 8 residues within 4Å: Chain E: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, D.413 Ligand excluded by PLIP DMS.55: 4 residues within 4Å: Chain E: W.309, E.421 Ligands: DMS.51, GOL.54 Ligand excluded by PLIP DMS.56: 5 residues within 4Å: Chain E: P.28, W.33, R.57, P.61, A.65 Ligand excluded by PLIP DMS.57: 5 residues within 4Å: Chain E: A.367, E.368, E.370, R.396, T.397 Ligand excluded by PLIP DMS.62: 5 residues within 4Å: Chain F: F.44, D.46, F.47, I.48 Ligands: XF2.61 Ligand excluded by PLIP DMS.63: 3 residues within 4Å: Chain F: E.159, R.257 Ligands: DMS.67 Ligand excluded by PLIP DMS.64: 8 residues within 4Å: Chain F: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: GOL.66, PEG.72 Ligand excluded by PLIP DMS.65: 8 residues within 4Å: Chain F: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, D.413 Ligand excluded by PLIP DMS.67: 4 residues within 4Å: Chain F: W.309, E.421 Ligands: DMS.63, GOL.66 Ligand excluded by PLIP DMS.68: 5 residues within 4Å: Chain F: P.28, W.33, R.57, P.61, A.65 Ligand excluded by PLIP DMS.69: 5 residues within 4Å: Chain F: A.367, E.368, E.370, R.396, T.397 Ligand excluded by PLIP

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: L.157, I.288, T.418, A.419, F.420, E.421 Ligands: DMS.4, DMS.7 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain A: S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain A: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.18: 8 residues within 4Å: Chain B: L.157, I.288, T.418, A.419, F.420, E.421 Ligands: DMS.16, DMS.19 Ligand excluded by PLIP GOL.22: 7 residues within 4Å: Chain B: S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligand excluded by PLIP GOL.23: 6 residues within 4Å: Chain B: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.30: 8 residues within 4Å: Chain C: L.157, I.288, T.418, A.419, F.420, E.421 Ligands: DMS.28, DMS.31 Ligand excluded by PLIP GOL.34: 7 residues within 4Å: Chain C: S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligand excluded by PLIP GOL.35: 6 residues within 4Å: Chain C: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.42: 8 residues within 4Å: Chain D: L.157, I.288, T.418, A.419, F.420, E.421 Ligands: DMS.40, DMS.43 Ligand excluded by PLIP GOL.46: 7 residues within 4Å: Chain D: S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligand excluded by PLIP GOL.47: 6 residues within 4Å: Chain D: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.54: 8 residues within 4Å: Chain E: L.157, I.288, T.418, A.419, F.420, E.421 Ligands: DMS.52, DMS.55 Ligand excluded by PLIP GOL.58: 7 residues within 4Å: Chain E: S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligand excluded by PLIP GOL.59: 6 residues within 4Å: Chain E: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.66: 8 residues within 4Å: Chain F: L.157, I.288, T.418, A.419, F.420, E.421 Ligands: DMS.64, DMS.67 Ligand excluded by PLIP GOL.70: 7 residues within 4Å: Chain F: S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligand excluded by PLIP GOL.71: 6 residues within 4Å: Chain F: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP

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

PEG.12: 9 residues within 4Å: Chain A: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 Ligands: DMS.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.289 Water bridges: A:L.261, A:I.288 PEG.24: 9 residues within 4Å: Chain B: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 Ligands: DMS.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.289 Water bridges: B:L.261, B:I.288 PEG.36: 9 residues within 4Å: Chain C: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 Ligands: DMS.28 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.289 Water bridges: C:L.261, C:I.288 PEG.48: 9 residues within 4Å: Chain D: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 Ligands: DMS.40 2 PLIP interactions: 2 interactions with chain D Water bridges: D:L.261, D:I.288 PEG.60: 9 residues within 4Å: Chain E: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 Ligands: DMS.52 2 PLIP interactions: 2 interactions with chain E Water bridges: E:L.261, E:I.288 PEG.72: 9 residues within 4Å: Chain F: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 Ligands: DMS.64 2 PLIP interactions: 2 interactions with chain F Water bridges: F:L.261, F:I.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pang, A.H. et al., Discovery and Mechanistic Analysis of Structurally Diverse Inhibitors of Acetyltransferase Eis among FDA-Approved Drugs. Biochemistry (2023)

Release Date

2023-02-01

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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