SMTL ID : 4orm.1

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM338 (N-[3,5-difluoro-4-(trifluoromethyl)phenyl]-5-methyl-2-(trifluoromethyl)[1,2,4]triazolo[1,5-a]pyrimidin-7-amine)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

monomer

Ligands

1 x 2V6: N-[3,5-difluoro-4-(trifluoromethyl)phenyl]-5-methyl-2-(trifluoromethyl)[1,2,4]triazolo[1,5-a]pyrimidin-7-amine(Non-covalent)

2V6.1: 19 residues within 4Å: Chain A: L.34, L.38, G.43, E.44, C.46, H.47, F.50, L.51, L.59, F.89, I.99, L.102, I.125, R.127, I.134, L.363, V.364, G.367, M.368 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.34, A:L.34, A:L.38 Hydrogen bonds: A:H.47, A:R.127 pi-Stacking: A:F.89

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 24 residues within 4Å: Chain A: A.86, A.87, G.88, K.91, G.110, T.111, I.125, I.134, N.136, C.138, N.204, K.261, S.289, N.290, T.291, S.309, G.310, L.313, S.337, G.338, G.339, Y.360, S.361 Ligands: ORO.3 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:I.125, A:I.134, A:N.136, A:Y.360 Hydrogen bonds: A:A.87, A:K.91, A:T.111, A:T.111, A:T.111, A:S.173, A:K.261, A:K.261, A:N.290, A:G.310, A:S.337, A:G.339, A:Y.360, A:S.361, A:S.361 Water bridges: A:A.87, A:G.338, A:G.338, A:G.338, A:I.340, A:Q.358 pi-Stacking: A:Y.360

1 x ORO: OROTIC ACID(Non-covalent)

ORO.3: 12 residues within 4Å: Chain A: K.91, N.136, C.138, G.139, F.140, N.204, S.207, P.208, N.209, N.290, T.291 Ligands: FMN.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.140 Hydrogen bonds: A:N.136, A:N.136, A:N.136, A:C.138, A:G.139, A:F.140, A:N.204, A:S.207, A:N.209, A:N.290, A:N.290, A:T.291 Salt bridges: A:K.91

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: E.237, N.243, D.244 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.237, A:D.244, A:D.244 Water bridges: A:E.245

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

SO4.5: 2 residues within 4Å: Chain A: E.26 Ligands: SO4.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.26 SO4.6: 6 residues within 4Å: Chain A: N.24, E.26, F.27, Y.61, T.63 Ligands: SO4.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.24, A:E.26, A:Y.61, A:Y.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deng, X. et al., Fluorine Modulates Species Selectivity in the Triazolopyrimidine Class of Plasmodium falciparum Dihydroorotate Dehydrogenase Inhibitors. J.Med.Chem. (2014)

Release Date

2014-06-04

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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