SMTL ID : 9di6.1

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM679 (ethyl 1,4-dimethyl-5-((6-(trifluoromethyl)pyridin-3-yl)methyl)-1H-pyrazole-3-carboxylate)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

monomer

Ligands

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

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 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:H.47, A:F.50, A:I.125, A:V.364 Hydrogen bonds: A:R.127 Salt bridges: A:R.127

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 29 residues within 4Å: Chain A: A.86, A.87, G.88, K.91, 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 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.125, A:N.136, A:Y.360 Hydrogen bonds: A:K.91, A:T.111, A:T.111, A:N.204, A:K.261, 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:S.173, A:G.338, A:G.338, A:I.340 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, S.137, C.138, G.139, F.140, N.204, S.207, P.208, N.209, N.290, T.291 Ligands: FMN.2 13 PLIP interactions: 13 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 Salt bridges: A:K.91

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.4: 3 residues within 4Å: Chain A: L.154, K.157, R.158 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.154 Hydrogen bonds: A:L.154, A:K.157 Salt bridges: A:K.157, A:R.158

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

LDA.5: 10 residues within 4Å: Chain A: R.156, Q.159, E.160, S.166, F.246, W.248, F.249, N.250, T.251, K.253 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.159, A:E.160, A:F.249

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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