SMTL ID : 5tbo.1

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM421

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

1 x 78Z: 2-(1,1-difluoroethyl)-5-methyl-N-[6-(trifluoromethyl)pyridin-3-yl][1,2,4]triazolo[1,5-a]pyrimidin-7-amine(Non-covalent)

78Z.1: 22 residues within 4Å: Chain A: L.34, C.37, 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, Y.360, L.363, V.364, G.367, M.368 Ligands: FMN.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.34, A:L.34, A:L.38, A:F.50, A:I.125, A:R.127, A:I.134, A:L.363 Hydrogen bonds: A:H.47, A:R.127 pi-Stacking: A:F.89 Halogen bonds: A:Y.360

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 29 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, F.140, S.173, N.204, K.261, S.289, N.290, T.291, S.309, G.310, L.313, S.337, G.338, G.339, I.340, L.359, Y.360, S.361 Ligands: 78Z.1, ORO.3 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:I.125, A:N.136 Hydrogen bonds: A:K.91, A:T.111, A:T.111, A:S.173, A:N.204, 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:I.340, A:Q.358, A:Q.358 pi-Stacking: A:Y.360

1 x ORO: OROTIC ACID(Non-covalent)

ORO.3: 9 residues within 4Å: Chain A: K.91, N.136, C.138, G.139, F.140, N.204, N.290, T.291 Ligands: FMN.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.140 Hydrogen bonds: A:N.136, A:N.136, A:C.138, A:G.139, A:F.140, A:N.204, A:N.290, A:N.290, A:T.291 Salt bridges: A:K.91

1 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)

LDA.4: 10 residues within 4Å: Chain A: E.26, L.29, Y.30, F.33, N.57, I.58, L.59, P.60, Y.61 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.33 Salt bridges: A:E.26 pi-Cation interactions: A:Y.61

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: K.55, G.93, V.94, I.96, N.151, L.154, F.155, R.158 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.93, A:F.155, A:R.158, A:R.158 Water bridges: A:K.55 GOL.6: 7 residues within 4Å: Chain A: E.26, F.27, P.60, Y.61, D.62, T.63 Ligands: LDA.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.61, A:Y.61, A:Y.61, A:T.63, A:T.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Phillips, M.A. et al., A Triazolopyrimidine-Based Dihydroorotate Dehydrogenase Inhibitor with Improved Drug-like Properties for Treatment and Prevention of Malaria. ACS Infect Dis (2016)

Release Date

2016-09-28

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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