SMTL ID : 8f4u.1

Crystal structure of acetyltransferase Eis from M. tuberculosis in complex with azelastine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-hexamer

Ligands

6 x XG0: 4-[(4-chlorophenyl)methyl]-2-[(4S)-1-methylazepan-4-yl]phthalazin-1(2H)-one(Non-covalent)

XG0.1: 12 residues within 4Å: Chain A: F.44, D.46, F.47, S.52, A.53, W.56, R.57, L.83, S.103, F.104, F.422 Ligands: GOL.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:D.46, A:A.53, A:W.56, A:W.56, A:W.56, A:W.56, A:F.104, A:F.104 Water bridges: A:D.46 XG0.9: 12 residues within 4Å: Chain B: F.44, D.46, F.47, S.52, A.53, W.56, R.57, L.83, S.103, F.104, F.422 Ligands: GOL.11 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:D.46, B:A.53, B:W.56, B:W.56, B:W.56, B:W.56, B:F.104, B:F.104 Water bridges: B:D.46 XG0.17: 12 residues within 4Å: Chain C: F.44, D.46, F.47, S.52, A.53, W.56, R.57, L.83, S.103, F.104, F.422 Ligands: GOL.19 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:D.46, C:A.53, C:W.56, C:W.56, C:W.56, C:W.56, C:F.104, C:F.104 Water bridges: C:D.46 XG0.25: 12 residues within 4Å: Chain D: F.44, D.46, F.47, S.52, A.53, W.56, R.57, L.83, S.103, F.104, F.422 Ligands: GOL.27 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:D.46, D:A.53, D:W.56, D:W.56, D:W.56, D:W.56, D:F.104, D:F.104 Water bridges: D:D.46 XG0.33: 12 residues within 4Å: Chain E: F.44, D.46, F.47, S.52, A.53, W.56, R.57, L.83, S.103, F.104, F.422 Ligands: GOL.35 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:D.46, E:A.53, E:W.56, E:W.56, E:W.56, E:W.56, E:F.104, E:F.104 Water bridges: E:D.46 XG0.41: 12 residues within 4Å: Chain F: F.44, D.46, F.47, S.52, A.53, W.56, R.57, L.83, S.103, F.104, F.422 Ligands: GOL.43 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:D.46, F:A.53, F:W.56, F:W.56, F:W.56, F:W.56, F:F.104, F:F.104 Water bridges: F:D.46

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP GOL.3: 9 residues within 4Å: Chain A: L.102, S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligands: XG0.1 Ligand excluded by PLIP GOL.4: 5 residues within 4Å: Chain A: R.262, I.288, T.418, A.419, E.421 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.10: 6 residues within 4Å: Chain B: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP GOL.11: 9 residues within 4Å: Chain B: L.102, S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligands: XG0.9 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain B: R.262, I.288, T.418, A.419, E.421 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain B: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain C: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP GOL.19: 9 residues within 4Å: Chain C: L.102, S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligands: XG0.17 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain C: R.262, I.288, T.418, A.419, E.421 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain C: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.26: 6 residues within 4Å: Chain D: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP GOL.27: 9 residues within 4Å: Chain D: L.102, S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligands: XG0.25 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain D: R.262, I.288, T.418, A.419, E.421 Ligand excluded by PLIP GOL.30: 6 residues within 4Å: Chain D: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.34: 6 residues within 4Å: Chain E: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP GOL.35: 9 residues within 4Å: Chain E: L.102, S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligands: XG0.33 Ligand excluded by PLIP GOL.36: 5 residues within 4Å: Chain E: R.262, I.288, T.418, A.419, E.421 Ligand excluded by PLIP GOL.38: 6 residues within 4Å: Chain E: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.42: 6 residues within 4Å: Chain F: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP GOL.43: 9 residues within 4Å: Chain F: L.102, S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligands: XG0.41 Ligand excluded by PLIP GOL.44: 5 residues within 4Å: Chain F: R.262, I.288, T.418, A.419, E.421 Ligand excluded by PLIP GOL.46: 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.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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.288, A:T.289 Water bridges: A:Q.417 PEG.13: 9 residues within 4Å: Chain B: 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 B Hydrogen bonds: B:I.288, B:T.289 Water bridges: B:Q.417 PEG.21: 9 residues within 4Å: Chain C: 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 C Hydrogen bonds: C:I.288, C:T.289 Water bridges: C:Q.417 PEG.29: 9 residues within 4Å: Chain D: L.261, H.269, I.287, I.288, T.289, H.290, D.293, P.294, Q.417 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.288 Water bridges: D:Q.417 PEG.37: 9 residues within 4Å: Chain E: L.261, H.269, I.287, I.288, T.289, H.290, D.293, P.294, Q.417 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:I.288 Water bridges: E:Q.417 PEG.45: 9 residues within 4Å: Chain F: L.261, H.269, I.287, I.288, T.289, H.290, D.293, P.294, Q.417 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:I.288 Water bridges: F:Q.417

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

DMS.7: 7 residues within 4Å: Chain A: P.92, G.93, R.328, G.329, Y.330, A.411, D.413 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.93 Water bridges: A:E.94 DMS.15: 7 residues within 4Å: Chain B: P.92, G.93, R.328, G.329, Y.330, A.411, D.413 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.93 Water bridges: B:E.94 DMS.23: 7 residues within 4Å: Chain C: P.92, G.93, R.328, G.329, Y.330, A.411, D.413 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.93 Water bridges: C:E.94 DMS.31: 7 residues within 4Å: Chain D: P.92, G.93, R.328, G.329, Y.330, A.411, D.413 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.93 Water bridges: D:E.94, D:D.413 DMS.39: 7 residues within 4Å: Chain E: P.92, G.93, R.328, G.329, Y.330, A.411, D.413 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.93 Water bridges: E:E.94, E:D.413 DMS.47: 7 residues within 4Å: Chain F: P.92, G.93, R.328, G.329, Y.330, A.411, D.413 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:G.93 Water bridges: F:E.94, F:D.413

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

SO4.8: 6 residues within 4Å: Chain A: R.113, R.114, G.115, L.116, L.117, R.118 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.113, A:R.114, A:G.115, A:L.116, A:L.117, A:R.118 SO4.16: 6 residues within 4Å: Chain B: R.113, R.114, G.115, L.116, L.117, R.118 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.113, B:R.114, B:G.115, B:L.116, B:L.117, B:R.118 SO4.24: 6 residues within 4Å: Chain C: R.113, R.114, G.115, L.116, L.117, R.118 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.113, C:R.114, C:G.115, C:L.116, C:L.117, C:R.118 SO4.32: 6 residues within 4Å: Chain D: R.113, R.114, G.115, L.116, L.117, R.118 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.113, D:R.114, D:G.115, D:L.116, D:L.117, D:R.118 SO4.40: 6 residues within 4Å: Chain E: R.113, R.114, G.115, L.116, L.117, R.118 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:R.113, E:R.114, E:G.115, E:L.116, E:L.117, E:R.118 SO4.48: 6 residues within 4Å: Chain F: R.113, R.114, G.115, L.116, L.117, R.118 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:R.113, F:R.114, F:G.115, F:L.116, F:L.117, F:R.118

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

2023-02-08

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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