SMTL ID : 9dik.2 (1 other biounit)

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM681 (N-cyclopropyl-1,4-dimethyl-5-((6-(trifluoromethyl)pyridin-3-yl)methyl)-1H-pyrazole-3-carboxamide)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x 01: N-cyclopropyl-1,4-dimethyl-5-{[6-(trifluoromethyl)pyridin-3-yl]methyl}-1H-pyrazole-3-carboxamide

01.1: 22 residues within 4Å: Chain A: Y.30, F.33, L.34, C.37, L.38, G.43, E.44, C.46, H.47, L.49, F.50, L.53, F.89, I.125, R.127, I.134, Y.360, L.363, V.364, G.367, M.368 Ligands: FMN.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.38, A:I.125, A:R.127, A:V.364 Hydrogen bonds: A:R.127

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: 01.1, OG6.3 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:I.125, A:N.136, A:Y.360 Hydrogen bonds: A:T.111, A:T.111, A:N.204, A:K.261, A:S.289, A:N.290, A:S.309, A:G.310, A:S.337, A:G.339, A:Y.360, A:S.361, A:S.361 Water bridges: A:A.87, A:E.108, A:G.338, A:G.338, A:G.338, A:Q.358, A:Q.358 pi-Stacking: A:Y.360

1 x OG6: 6-[bis(oxidanyl)methyl]-5~{H}-pyrimidine-2,4-dione(Non-covalent)

OG6.3: 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:N.209, A:N.290, A:N.290, A:T.291 Water bridges: A:S.207 Salt bridges: A:K.91

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 5 residues within 4Å: Chain A: K.314, D.315, T.318, E.348, K.349 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.315, A:T.318, A:E.348 NA.5: 4 residues within 4Å: Chain A: E.218, A.219, Q.270, E.273 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.219, A:E.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nie, Z. et al., Structure-Based Discovery and Development of Highly Potent Dihydroorotate Dehydrogenase Inhibitors for Malaria Chemoprevention. J.Med.Chem. (2025)

Release Date

2025-01-01

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Dihydroorotate dehydrogenase (quinone), mitochondrial

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