7KZ4

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM705 (N-(1-(1H-1,2,4-triazol-3-yl)ethyl)-3-methyl-4-(1-(6-(trifluoromethyl)pyridin-3-yl)cyclopropyl)-1H-pyrrole-2-carboxamide)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Potent Antimalarials with Development Potential Identified by Structure-Guided Computational Optimization of a Pyrrole-Based Dihydroorotate Dehydrogenase Inhibitor Series.

Palmer, M.J.Deng, X.Watts, S.Krilov, G.Gerasyuto, A.Kokkonda, S.El Mazouni, F.White, J.White, K.L.Striepen, J.Bath, J.Schindler, K.A.Yeo, T.Shackleford, D.M.Mok, S.Deni, I.Lawong, A.Huang, A.Chen, G.Wang, W.Jayaseelan, J.Katneni, K.Patil, R.Saunders, J.Shahi, S.P.Chittimalla, R.Angulo-Barturen, I.Jimenez-Diaz, M.B.Wittlin, S.Tumwebaze, P.K.Rosenthal, P.J.Cooper, R.A.Aguiar, A.C.C.Guido, R.V.C.Pereira, D.B.Mittal, N.Winzeler, E.A.Tomchick, D.R.Laleu, B.Burrows, J.N.Rathod, P.K.Fidock, D.A.Charman, S.A.Phillips, M.A.

(2021) J Med Chem 64: 6085-6136

  • DOI: 10.1021/acs.jmedchem.1c00173
  • Primary Citation of Related Structures:  
    7KYK, 7KYV, 7KYY, 7KZ4, 7KZY, 7L01, 7L0K

  • PubMed Abstract: 
  • Dihydroorotate dehydrogenase (DHODH) has been clinically validated as a target for the development of new antimalarials. Experience with clinical candidate triazolopyrimidine DSM265 ( 1 ) suggested that DHODH inhibitors have great potential for use in prophylaxis, which represents an unmet need in the malaria drug discovery portfolio for endemic countries, particularly in areas of high transmission in Africa ...

    Dihydroorotate dehydrogenase (DHODH) has been clinically validated as a target for the development of new antimalarials. Experience with clinical candidate triazolopyrimidine DSM265 ( 1 ) suggested that DHODH inhibitors have great potential for use in prophylaxis, which represents an unmet need in the malaria drug discovery portfolio for endemic countries, particularly in areas of high transmission in Africa. We describe a structure-based computationally driven lead optimization program of a pyrrole-based series of DHODH inhibitors, leading to the discovery of two candidates for potential advancement to preclinical development. These compounds have improved physicochemical properties over prior series frontrunners and they show no time-dependent CYP inhibition, characteristic of earlier compounds. Frontrunners have potent antimalarial activity in vitro against blood and liver schizont stages and show good efficacy in Plasmodium falciparum SCID mouse models. They are equally active against P. falciparum and Plasmodium vivax field isolates and are selective for Plasmodium DHODHs versus mammalian enzymes.


    Organizational Affiliation

    Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase (quinone), mitochondrialA, B401Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PFF0160c
EC: 1.3.5.2
UniProt
Find proteins for Q08210 (Plasmodium falciparum (isolate 3D7))
Explore Q08210 
Go to UniProtKB:  Q08210
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08210
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
XC7 (Subject of Investigation/LOI)
Query on XC7

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
3-methyl-N-[(1R)-1-(1H-1,2,4-triazol-3-yl)ethyl]-4-{1-[6-(trifluoromethyl)pyridin-3-yl]cyclopropyl}-1H-pyrrole-2-carboxamide
C19 H19 F3 N6 O
JUBPRXDFKLPILK-LLVKDONJSA-N
 Ligand Interaction
ORO (Subject of Investigation/LOI)
Query on ORO

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.914α = 90
b = 157.99β = 107.012
c = 63.152γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI103947

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-19
    Type: Initial release
  • Version 1.1: 2021-12-08
    Changes: Database references