SMTL ID : 9diz.1

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM959 (6-cyclopropyl-2,4-dimethyl-3-((6-(trifluoromethyl)pyridin-3-yl)methyl)-2,6-dihydro-7H-pyrazolo[3,4-c]pyridin-7-one)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

monomer

Ligands

1 x 01: 6-cyclopropyl-2,4-dimethyl-3-{[6-(trifluoromethyl)pyridin-3-yl]methyl}-2,6-dihydro-7H-pyrazolo[3,4-c]pyridin-7-one

01.1: 21 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 Ligands: FMN.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:H.47, A:F.50, A:F.89, A:I.125, A:I.125, A:V.364 Hydrogen bonds: A:R.127, A:R.127 Halogen bonds: A:Y.30

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 28 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, 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: 01.1, OG6.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.125, A:N.136 Hydrogen bonds: A:A.87, A:K.91, A:T.111, A:T.111, A:S.173, A:N.204, A:K.261, A:S.309, A:G.310, A:S.337, A:G.339, A:I.340, A:Y.360, A:S.361, A:S.361 pi-Stacking: A:Y.360

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

OG6.3: 13 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, G.307 Ligands: FMN.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.136, A:N.136, A:C.138, A:G.139, A:N.204, A:N.209, A:N.290, A:N.290, A:T.291 Salt bridges: A:K.91

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
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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