SMTL ID : 5ae2.2 (1 other biounit)

Ether Lipid-Generating Enzyme AGPS in complex with inhibitor 1e

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x FYC: 3-(2-fluorophenyl)-2-methyl-N-((2-oxo-2,3-dihydro-1H-benzo[d]imidazol-5-yl)methyl)acrylamide(Non-covalent)

FYC.1: 15 residues within 4Å: Chain A: D.303, I.511, A.512, M.514, R.515, G.525, E.526, S.527, Y.578, Y.580, F.581, A.582, H.616, H.617 Ligands: FAD.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:R.515, A:A.582 Hydrogen bonds: A:D.303, A:S.527, A:Y.578, A:H.617 Water bridges: A:A.512 FYC.4: 14 residues within 4Å: Chain B: D.303, I.511, A.512, M.514, R.515, G.525, E.526, S.527, Y.578, Y.580, A.582, H.616, H.617 Ligands: FAD.5 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.511, B:R.515, B:R.515, B:Y.580, B:A.582 Hydrogen bonds: B:D.303, B:D.303, B:Y.578, B:H.617 Water bridges: B:A.512, B:R.515, B:R.566

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.2: 36 residues within 4Å: Chain A: W.96, H.189, P.234, I.235, G.236, G.237, G.238, T.239, S.240, V.241, G.244, L.245, T.260, A.280, P.302, D.303, S.304, S.308, T.309, G.311, G.312, W.313, S.315, T.316, A.318, S.319, E.368, G.369, G.372, V.373, I.374, A.512, H.616, N.654, N.656 Ligands: FYC.1 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:W.96, A:W.96, A:H.189, A:D.303, A:A.512 Hydrogen bonds: A:G.236, A:G.237, A:G.238, A:T.239, A:T.239, A:T.239, A:S.240, A:D.303, A:S.304, A:S.304, A:T.309, A:T.309, A:G.312, A:S.315, A:T.316, A:S.319, A:S.319, A:G.369, A:I.374, A:I.374, A:N.654, A:N.656 Water bridges: A:G.311, A:T.316, A:H.617 FAD.5: 36 residues within 4Å: Chain B: W.96, H.189, P.234, I.235, G.236, G.237, G.238, T.239, S.240, V.241, G.244, L.245, T.260, A.280, P.302, D.303, S.304, S.308, T.309, G.311, G.312, W.313, S.315, T.316, A.318, S.319, E.368, G.369, G.372, V.373, I.374, A.512, H.616, N.654, N.656 Ligands: FYC.4 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:W.96, B:W.96, B:H.189, B:D.303, B:A.512 Hydrogen bonds: B:G.236, B:G.237, B:G.238, B:T.239, B:T.239, B:S.240, B:D.303, B:S.304, B:S.304, B:T.309, B:G.312, B:S.315, B:S.319, B:S.319, B:G.369, B:I.374, B:I.374, B:N.654, B:N.656 Water bridges: B:T.260, B:T.316, B:T.316, B:H.617

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

SO4.3: 8 residues within 4Å: Chain A: I.325, A.414, P.415, A.416, F.470, E.471, V.477, H.480 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.414, A:A.416, A:E.471, A:E.471 Salt bridges: A:H.480 SO4.6: 7 residues within 4Å: Chain B: I.325, P.415, A.416, F.470, E.471, V.477, H.480 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.416, B:E.471, B:E.471 Salt bridges: B:H.480

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Piano, V. et al., Discovery of Inhibitors for the Ether Lipid-Generating Enzyme Agps as Anti-Cancer Agents. Acs Chem.Biol. (2015)

Release Date

2015-09-09

Peptides

ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL

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