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Structure paper

TitleStructure-Based Discovery and Development of Highly Potent Dihydroorotate Dehydrogenase Inhibitors for Malaria Chemoprevention.
Journal, issue, pagesJ. Med. Chem., Vol. 68, Page 590-637, Year 2025
Publish dateSep 5, 2024 (structure data deposition date)
AuthorsNie, Z. / Bonnert, R. / Tsien, J. / Deng, X. / Higgs, C. / El Mazouni, F. / Zhang, X. / Li, R. / Ho, N. / Feher, V. ...Nie, Z. / Bonnert, R. / Tsien, J. / Deng, X. / Higgs, C. / El Mazouni, F. / Zhang, X. / Li, R. / Ho, N. / Feher, V. / Paulsen, J. / Shackleford, D.M. / Katneni, K. / Chen, G. / Ng, A.C.F. / McInerney, M. / Wang, W. / Saunders, J. / Collins, D. / Yan, D. / Li, P. / Campbell, M. / Patil, R. / Ghoshal, A. / Mondal, P. / Kundu, A. / Chittimalla, R. / Mahadeva, M. / Kokkonda, S. / White, J. / Das, R. / Mukherjee, P. / Angulo-Barturen, I. / Jimenez-Diaz, M.B. / Malmstrom, R. / Lawrenz, M. / Rodriguez-Granillo, A. / Rathod, P.K. / Tomchick, D.R. / Palmer, M.J. / Laleu, B. / Qin, T. / Charman, S.A. / Phillips, M.A.
External linksJ. Med. Chem. / PubMed:39710971
MethodsX-ray diffraction
Resolution2.1 - 3.3 Å
Structure data

PDB-9di6:
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)
Method: X-RAY DIFFRACTION / Resolution: 2.41 Å

PDB-9dik:
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)
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-9diz:
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)
Method: X-RAY DIFFRACTION / Resolution: 3.1 Å

PDB-9dko:
Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM1010 (6-cyclopropyl-2,4-dimethyl-3-(4-(trifluoromethyl)benzyl)-2,6-dihydro-7H-pyrazolo[3,4-c]pyridin-7-one)
Method: X-RAY DIFFRACTION / Resolution: 3 Å

PDB-9dkq:
Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM1153 (4,6-dicyclopropyl-3-(3-fluoro-4-(trifluoromethyl)benzyl)-2-methyl-2,6-dihydro-7H-pyrazolo[3,4-d]pyridazin-7-one)
Method: X-RAY DIFFRACTION / Resolution: 3.15 Å

PDB-9dky:
Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM1174 (3-((7-azaspiro[3.5]nonan-7-yl)methyl)-4-cyclopropyl-6-ethyl-2-methyl-2,6-dihydro-7H-pyrazolo[3,4-c]pyridin-7-one)
Method: X-RAY DIFFRACTION / Resolution: 3.3 Å

PDB-9dlk:
Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM1398 ((S)-3-(amino(3-chloro-4-(trifluoromethyl)phenyl)(cyclopropyl)methyl)-6-cyclopropyl-2-methyl-2,6-dihydro-7H-pyrazolo[3,4-d]pyridazin-7-one)
Method: X-RAY DIFFRACTION / Resolution: 2.9 Å

PDB-9dly:
Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM1211 ((R)-3-(amino(6-(trifluoromethyl)pyridin-3-yl)methyl)-4-cyclopropyl-6-ethyl-2-methyl-2,6-dihydro-7H-pyrazolo[3,4-c]pyridin-7-one)
Method: X-RAY DIFFRACTION / Resolution: 3.1 Å

Chemicals

PDB-1a51:
LOOP D/LOOP E ARM OF E. COLI 5S RRNA, NMR, 9 STRUCTURES

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

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

ChemComp-CIT:
CITRIC ACID

ChemComp-LDA:
LAURYL DIMETHYLAMINE-N-OXIDE / LDAO, detergent*YM

ChemComp-HOH:
WATER

PDB-1a52:
ESTROGEN RECEPTOR ALPHA LIGAND-BINDING DOMAIN COMPLEXED TO ESTRADIOL

ChemComp-NA:
Unknown entry

PDB-1a53:
COMPLEX OF INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE FROM SULFOLOBUS SOLFATARICUS WITH INDOLE-3-GLYCEROLPHOSPHATE AT 2.0 A RESOLUTION

PDB-1a5p:
C[40,95]A VARIANT OF BOVINE PANCREATIC RIBONUCLEASE A

PDB-1a5q:
P93A VARIANT OF BOVINE PANCREATIC RIBONUCLEASE A

PDB-1a59:
COLD-ACTIVE CITRATE SYNTHASE

PDB-1a6d:
THERMOSOME FROM T. ACIDOPHILUM

ChemComp-ACY:
ACETIC ACID

PDB-1a6e:
THERMOSOME-MG-ADP-ALF3 COMPLEX

Source
  • plasmodium falciparum 3d7 (eukaryote)
KeywordsOXIDOREDUCTASE/INHIBITOR / inhibitor / Alpha-Beta Barrel / OXIDOREDUCTASE / Flavoprotein / OXIDOREDUCTASE-INHIBITOR complex

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