SMTL ID : 5fi8.1

Crystal structure of plasmodium falciparum dihydroorotate dehydrogenase bounded with DSM422 (Tetrahydro-2-naphthyl and 2-indanyl triazolopyrimidine)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

monomer

Ligands

1 x 5Y5: 2-[1,1-bis(fluoranyl)ethyl]-~{N}-[(2~{S})-7-bromanyl-1,2,3,4-tetrahydronaphthalen-2-yl]-5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-amine(Non-covalent)

5Y5.1: 24 residues within 4Å: Chain A: L.34, C.37, L.38, G.43, E.44, C.46, H.47, F.50, L.51, G.54, L.59, F.89, C.95, I.99, L.102, I.125, R.127, I.134, Y.360, L.363, V.364, G.367, M.368 Ligands: FMN.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.50, A:L.59, A:F.89, A:F.89, A:L.102, A:I.125, A:R.127, A:I.134 Hydrogen bonds: A:H.47, A:R.127 Halogen bonds: A:C.95

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 30 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, C.362 Ligands: 5Y5.1, ORO.3 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.125, A:N.136 Hydrogen bonds: A:K.91, A:T.111, A:T.111, A:N.204, A:K.261, A:N.290, A:G.310, A:G.339, A:Y.360, A:S.361, A:S.361 Water bridges: A:A.87, A:T.111, A:T.111, A:S.337, 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: 9 residues within 4Å: Chain A: E.26, L.29, Y.30, F.33, N.57, I.58, L.59, P.60, Y.61 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.30, A:Y.30 Salt bridges: A:E.26 pi-Cation interactions: A:Y.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kokkonda, S. et al., Tetrahydro-2-naphthyl and 2-Indanyl Triazolopyrimidines Targeting Plasmodium falciparum Dihydroorotate Dehydrogenase Display Potent and Selective Antimalarial Activity. J.Med.Chem. (2016)

Release Date

2016-05-18

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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