Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44.82 kDa 
• Atom Count: 3177 
• Residue Count: 364 
• Unique protein chains: 1

2FPY

Dual binding mode of a novel series of DHODH inhibitors

• DOI: 10.2210/pdb2FPY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-01-17 Released: 2007-01-23 
• Deposition Author(s): Baumgartner, R., Leban, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.200 
• R-Value Work: 0.181 

Literature

Dual binding mode of a novel series of DHODH inhibitors.

Baumgartner, R., Walloschek, M., Kralik, M., Gotschlich, A., Tasler, S., Mies, J., Leban, J.

(2006) J Med Chem 49: 1239-1247

• PubMed: 16480261 
• DOI: 10.1021/jm0506975
• Primary Citation of Related Structures:  
  2BXV, 2FPY, 2FPV, 2FPT, 2FQI


• PubMed Abstract: 
  

Human dihydroorotate dehydrogenase (DHODH) represents an important target for the treatment of hyperproliferative and inflammatory diseases. In the cell DHODH catalyzes the rate-limiting step of the de novo pyrimidine biosynthesis. DHODH inhibition results in beneficial immunosuppressant and antiproliferative effects in diseases such as rheumatoid arthritis. Here, we present high-resolution X-ray structures of human DHODH in complex with a novel class of low molecular weight compounds that inhibit the enzyme in the nanomolar range. Some compounds showed an interesting dual binding mode within the same cocrystal strongly depending on the nature of chemical substitution. Measured in vitro activity data correlated with the prevailing mode of binding and explained the observed structure-activity relationship. Additionally, the X-ray data confirmed the competitive nature of the inhibitors toward the putative ubiquinone binding site and will guide structure-based design and synthesis of molecules with higher activity.

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Organizational Affiliation: 

4SC AG, Am Klopferspitz 19a, 82152 Martinsried, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase, mitochondrial precursor	A	395	Homo sapiens	Mutation(s): 0  Gene Names: DHODH EC: 1.3.3.1 (PDB Primary Data), 1.3.5.2 (UniProt)
Find proteins for Q02127 (Homo sapiens) Explore Q02127  Go to UniProtKB:  Q02127
NIH Common Fund Data Resources
PHAROS  Q02127 GTEx  ENSG00000102967

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	A	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
ILF	A	3-({[3,5-DIFLUORO-3'-(TRIFLUOROMETHOXY)BIPHENYL-4-YL]AMINO}CARBONYL)THIOPHENE-2-CARBOXYLIC ACID C19 H10 F5 N O4 S CGNHUSCKOHDSMR-UHFFFAOYSA-N
ORO	A	OROTIC ACID C5 H4 N2 O4 PXQPEWDEAKTCGB-UHFFFAOYSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ILF	IC50:  2   nM  BindingDB
ILF	IC50:  2   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.200 
• R-Value Work: 0.181 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.295	α = 90
b = 90.295	β = 90
c = 122.695	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-01-17 
• Released Date: 2007-01-23 
Deposition Author(s): Baumgartner, R., Leban, J.

Revision History 

• Version 1.0: 2007-01-23
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance