9DKQ | pdb_00009dkq

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)

• PDB DOI: https://doi.org/10.2210/pdb9DKQ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2024-09-09 Released: 2025-01-01 
• Deposition Author(s): Deng, X., Tomchic, D., Phillips, M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.210 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.173 (Depositor) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Structure-Based Discovery and Development of Highly Potent Dihydroorotate Dehydrogenase Inhibitors for Malaria Chemoprevention.

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.

(2025) J Med Chem 68: 590-637

• PubMed: 39710971 
• DOI: https://doi.org/10.1021/acs.jmedchem.4c02394
• Primary Citation Related Structures: 
  9DI6, 9DIK, 9DIZ, 9DKO, 9DKQ, 9DKY, 9DLK, 9DLY


• PubMed Abstract: 
  

  Malaria remains a serious global health challenge, yet treatment and control programs are threatened by drug resistance. Dihydroorotate dehydrogenase (DHODH) was clinically validated as a target for treatment and prevention of malaria through human studies with DSM265, but currently no drugs against this target are in clinical use. We used structure-based computational tools including free energy perturbation (FEP+) to discover highly ligand efficient, potent, and selective pyrazole-based Plasmodium DHODH inhibitors through a scaffold hop from a pyrrole-based series. Optimized pyrazole-based compounds were identified with low nM-to-pM Plasmodium falciparum cell potency and oral activity in a humanized SCID mouse malaria infection model. The lead compound DSM1465 is more potent and has improved absorption, distribution, metabolism and excretion/pharmacokinetic (ADME/PK) properties compared to DSM265 that support the potential for once-monthly chemoprevention at a low dose. This compound meets the objective of identifying compounds with potential to be used for monthly chemoprevention in Africa to support malaria elimination efforts.

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Organizational Affiliation: 
• Schrödinger Inc., 1540 Broadway, New York, New York 10036, United States.
MMV Medicines for Malaria Venture, ICC, Route de Pré-Bois 20, 1215 Geneva, Switzerland.
Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States.
Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia.
TCGLS, Block BN, Plot 7, Salt Lake Electronics Complex, Sector V, Kolkata 700091, West Bengal, India.
Syngene Scientific Solutions Limited, KSP 9000 Campus, Plot No. 7, Neovantage, Synergy Square 2, Kolthur Village, Shameerpet Mandal, Medchal Malkajgiri District, Hyderabad 500 078, Telangana, India.
Department of Chemistry, University of Washington, Seattle, Washington 98195, United States.
The Art of Discovery, Biscay Science and Technology Park, Astondo Bidea, BIC Bizkaia Bd 612, Derio, 48160 Bizkaia, Basque Country, Spain.
Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 46.41 kDa 
• Atom Count: 3,022 
• Modeled Residue Count: 371 
• Deposited Residue Count: 401 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase (quinone), mitochondrial	A	401	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PFF0160c EC: 1.3.5.2 Membrane Entity: Yes
UniProt
Find proteins for Q08210 (Plasmodium falciparum (isolate 3D7)) Explore Q08210  Go to UniProtKB:  Q08210

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
A1A5Q (Subject of Investigation/LOI)	B [auth A]	4,6-dicyclopropyl-3-{[3-fluoro-4-(trifluoromethyl)phenyl]methyl}-2-methyl-2,6-dihydro-7H-pyrazolo[3,4-d]pyridazin-7-one C20 H18 F4 N4 O YHZZQODDECZIPY-UHFFFAOYSA-N
OG6	D [auth A]	6-[bis(oxidanyl)methyl]-5~{H}-pyrimidine-2,4-dione C5 H6 N2 O4 DUGHQFVNXIWPEA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.210 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.173 (Depositor) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.615	α = 90
b = 85.615	β = 90
c = 140.161	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-01 
Deposition Author(s): Deng, X., Tomchic, D., Phillips, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI103947

Revision History  

• Version 1.0: 2025-01-01
  Type: Initial release
  
• Version 1.1: 2025-01-22
  Changes: Database references