9N6Q | pdb_00009n6q

Crystal structure of dihydroorotate dehydrogenase from Leishmania braziliensis in complex with 5-(4-hydroxy-3-methoxybenzyl)pyrimidine-2,4,6(1H,3H,5H)-trione


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.210 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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Literature

Barbituric Acid Derivatives as Covalent Inhibitors of Leishmania braziliensis Dihydroorotate Dehydrogenase.

Froes, T.Q.Alegbejo Price, T.O.Fleck Godoi, B.Vaidergorn, M.M.Dos Santos, T.Leite, P.I.P.Silva, D.G.Dias da Purificacao, A.Loch, L.Schenkman, S.Kratz, J.M.da Silva Emery, F.Nonato, M.C.

(2025) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00462
  • Primary Citation of Related Structures:  
    9CB8, 9N67, 9N68, 9N6O, 9N6Q

  • PubMed Abstract: 

    Covalent drug design applied to parasite proteins enables selective therapies by targeting nucleophilic residues of macromolecules. We present the first covalent inhibitors of Leishmania braziliensis dihydroorotate dehydrogenase ( Lb DHODH), a key enzyme in pyrimidine biosynthesis with a reactive cysteine (Cys 131 ) in its active site. From barbituric acid derivatives, we discovered 2i as a Lb DHODH inhibitor with leishmanicidal activity, exhibiting an IC 5 0 of 0.5 ± 0.1 μM, a K inact /K I of 767 M -1 s -1 , no inhibition of the human ortholog, and an EC 5 0 of 11 ± 5 μM in L. braziliensis promastigotes, with no cytotoxicity in THP-1 cells and good passive permeability. X-ray crystallography confirms covalent bond formation with Cys 131 and reveals active-site rearrangements. These findings support the proposed covalent inhibition mechanism and provide structural insights for further optimization. Our study validates Lb DHODH as a promising target for leishmaniasis therapy and highlights the potential of covalent inhibition in antiparasitic drug discovery.


  • Organizational Affiliation
    • Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto, SP 14040-903, Brazil.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase
A, B
347Leishmania braziliensisMutation(s): 0 
Gene Names: DHODHLBRM_16_0550
EC: 1.3.3.1 (PDB Primary Data), 1.3.98.1 (UniProt)
UniProt
Find proteins for E9AI53 (Leishmania braziliensis)
Explore E9AI53 
Go to UniProtKB:  E9AI53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9AI53
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
A1BWI (Subject of Investigation/LOI)
Query on A1BWI

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
5-ethyl-1,3-diazinane-2,4,6-trione
C6 H8 N2 O3
FMTLDVACNZDTQL-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
J [auth B],
K [auth B],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.210 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.72α = 90
b = 105.47β = 90
c = 106.12γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2019/ 25532-1
National Institutes of Health/National Cancer Institute (NIH/NCI)United States1R01AI160379-01

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-23
    Type: Initial release
  • Version 1.1: 2025-07-30
    Changes: Database references