Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44817.23 
• Atom Count: 2886 
• Residue Count: 395 
• 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)


• 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 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, 2FQI, 2FPV, 2FPT


• 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Dihydroorotate dehydrogenase, mitochondrial precursor	A	395	Homo sapiens	Mutation(s): 0  Gene Names: DHODH EC: 1.3.5.2
Find proteins for Q02127 (Homo sapiens) Go to Gene View: DHODH Go to UniProtKB:  Q02127

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
FMN	A	FLAVIN MONONUCLEOTIDE RIBOFLAVIN MONOPHOSPHATE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ILF	IC50: 2 nM (100) BINDINGDB
ILF	IC50: 2 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 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 = 90.00
b = 90.295	β = 90.00
c = 122.695	γ = 120.00

Software Package:

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

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance