Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 40.96 kDa 
• Atom Count: 3165 
• Modelled Residue Count: 361 
• Deposited Residue Count: 367 
• Unique protein chains: 1

3F1Q

Human dihydroorotate dehydrogenase in complex with a leflunomide derivative inhibitor 1

• PDB DOI: 10.2210/pdb3F1Q/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-10-28 Released: 2009-06-09 
• Deposition Author(s): Heikkila, T., Davies, M., McConkey, G.A., Fishwick, C.W.G., Parsons, M.R., Johnson, A.P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.199 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 

Literature

Structure-based design, synthesis, and characterization of inhibitors of human and Plasmodium falciparum dihydroorotate dehydrogenases

Davies, M., Heikkila, T., McConkey, G.A., Fishwick, C.W.G., Parsons, M.R., Johnson, A.P.

(2009) J Med Chem 52: 2683-2693

• PubMed: 19351152 
• DOI: 10.1021/jm800963t
• Primary Citation of Related Structures:  
  3F1Q, 3FJ6, 3FJL, 3G0U, 3G0X


• PubMed Abstract: 
  

Pyrimidine biosynthesis is an attractive drug target in a variety of organisms, including humans and the malaria parasite Plasmodium falciparum. Dihydroorotate dehydrogenase, an enzyme catalyzing the only redox reaction of the pyrimidine biosynthesis pathway, is a well-characterized target for chemotherapeutical intervention. In this study, we have applied SPROUT-LeadOpt, a software package for structure-based drug discovery and lead optimization, to improve the binding of the active metabolite of the anti-inflammatory drug leflunomide to the target cavities of the P. falciparum and human dihydroorotate dehydrogenases. Following synthesis of a library of compounds based upon the SPROUT-optimized molecular scaffolds, a series of inhibitors generally showing good inhibitory activity was obtained, in keeping with the SPROUT-LeadOpt predictions. Furthermore, cocrystal structures of five of these SPROUT-designed inhibitors bound in the ubiquinone binding cavity of the human dihydroorotate dehydrogenase are also analyzed.

---

Organizational Affiliation: 

School of Chemistry, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase	A	367	Homo sapiens	Mutation(s): 0  Gene Names: DHODH EC: 1.3.3.1 (PDB Primary Data), 1.3.5.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q02127 (Homo sapiens) Explore Q02127  Go to UniProtKB:  Q02127
PHAROS:  Q02127

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
BCE	D [auth A]	(2Z)-N-biphenyl-4-yl-2-cyano-3-hydroxybut-2-enamide C17 H14 N2 O2 MUVPBAIVOHJDOC-VBKFSLOCSA-N
ORO	C [auth A]	OROTIC ACID C5 H4 N2 O4 PXQPEWDEAKTCGB-UHFFFAOYSA-N
SO4	G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACY	E [auth A], F [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BCE	Binding MOAD:  3F1Q	IC50: 117 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.199 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.696	α = 90
b = 90.696	β = 90
c = 122.95	γ = 120

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-10-28 
• Released Date: 2009-06-09 
Deposition Author(s): Heikkila, T., Davies, M., McConkey, G.A., Fishwick, C.W.G., Parsons, M.R., Johnson, A.P.

Revision History  

• Version 1.0: 2009-06-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance