Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 78.07 kDa 
• Atom Count: 5601 
• Residue Count: 627 
• Unique protein chains: 1

4EF8

Crystal structure of dihydroorotate dehydrogenase from Leishmania major in complex with Phenyl isothiocyanate

• DOI: 10.2210/pdb4EF8/pdb

• Classification: Oxidoreductase/Oxidoreductase inhibitor
• Organism(s): Leishmania major
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-29 Released: 2012-12-12 
• Deposition Author(s): Pinheiro, M.P., Emery, F.S., Nonato, M.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.194 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 

Literature

Target sites for the design of anti-trypanosomatid drugs based on the structure of dihydroorotate dehydrogenase.

Pinheiro, M.P., Emery, F.S., Nonato, M.C.

(2013) Curr Pharm Des 19: 2615-2627

• PubMed: 23116399 
• DOI: 10.2174/1381612811319140011
• Primary Citation of Related Structures:  
  4EF8, 4EF9


• PubMed Abstract: 
  

Trypanosomatids consist of a large group of flagellated parasitic protozoa, including parasites from the genera Leishmania and Trypanosoma, responsible for causing infections in millions of humans worldwide and for which currently no appropriate therapy is available. The significance of pyrimidines in cellular metabolism makes their de novo and salvage pathways ideal druggable targets for pharmacological intervention and open an opportunity for pharmaceutical innovation. In the current review, we discuss the merits in targeting the enzyme dihydroorotate dehydrogenase (DHODH), a flavin-dependent enzyme that catalyzes the fourth and only redox step in pyrimidine de novo biosynthesis, as a strategy for the development of efficient therapeutic strategies for trypanosomatid-related diseases.We also describe the advances and perspectives from the structural biology point of view in order to unravel the structure-function relationship of trypanosomatid DHODHs, and to identify and validate target sites for drug development.

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Organizational Affiliation: 

Laboratorio de Cristalografia de Proteinas, Departamento de Fisica e Quimica, Faculdade de Ciencias Farmaceuticas de Ribeirao Preto, USP., Av. Cafe S/N, Monte Alegre, Ribeirao Preto, S.P. Brazil.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase	A, B	354	Leishmania major	Mutation(s): 0  Gene Names: DHODH, lmjf16.0530, LMJF_16_0530 EC: 1.3.3.1 (PDB Primary Data), 1.3.98.1 (UniProt)
Find proteins for Q4QEW7 (Leishmania major) Explore Q4QEW7  Go to UniProtKB:  Q4QEW7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	A, B	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
0FI	A, B	N-phenylthioformamide C7 H7 N S UNRRVOATHRPYDX-UHFFFAOYSA-N
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.194 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.19	α = 90
b = 144.19	β = 90
c = 69.87	γ = 120

Software Package:

Software Name	Purpose
NatXray	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-03-29 
• Released Date: 2012-12-12 
Deposition Author(s): Pinheiro, M.P., Emery, F.S., Nonato, M.C.

Revision History 

• Version 1.0: 2012-12-12
  Type: Initial release
  
• Version 1.1: 2013-05-22
  Changes: Database references