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 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.95 kDa 
• Atom Count: 3252 
• Modelled Residue Count: 365 
• Deposited Residue Count: 365 
• Unique protein chains: 1

2WV8

Complex of human dihydroorotate dehydrogenase with the inhibitor 221290

• PDB DOI: 10.2210/pdb2WV8/pdb

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


• Deposited: 2009-10-15 Released: 2010-08-25 
• Deposition Author(s): Walse, B., Svensson, B., Fritzson, I., Dahlberg, L., Wellmar, U., Al-Karadaghi, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.201 
• R-Value Work: 0.185 
• R-Value Observed: 0.185 

Literature

Inhibition of Human Dhodh by 4-Hydroxycoumarins, Fenamic Acids, and N-(Alkylcarbonyl)Anthranilic Acids Identified by Structure-Guided Fragment Selection.

Fritzson, I., Svensson, B., Al-Karadaghi, S., Walse, B., Wellmar, U., Nilsson, U.J., Da Graca Thrige, D., Jonsson, S.

(2010) ChemMedChem 5: 608

• PubMed: 20183850 
• DOI: 10.1002/cmdc.200900454
• Primary Citation of Related Structures:  
  2WV8


• PubMed Abstract: 
  

A strategy that combines virtual screening and structure-guided selection of fragments was used to identify three unexplored classes of human DHODH inhibitor compounds: 4-hydroxycoumarins, fenamic acids, and N-(alkylcarbonyl)anthranilic acids. Structure-guided selection of fragments targeting the inner subsite of the DHODH ubiquinone binding site made these findings possible with screening of fewer than 300 fragments in a DHODH assay. Fragments from the three inhibitor classes identified were subsequently chemically expanded to target an additional subsite of hydrophobic character. All three classes were found to exhibit distinct structure-activity relationships upon expansion. The novel N-(alkylcarbonyl)anthranilic acid class shows the most promising potency against human DHODH, with IC(50) values in the low nanomolar range. The structure of human DHODH in complex with an inhibitor of this class is presented.

---

Organizational Affiliation: 

Active Biotech Research AB, Box 724, 220 07 Lund, Sweden. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIHYDROOROTATE DEHYDROGENASE, MITOCHONDRIAL	A	365	Homo sapiens	Mutation(s): 0  Gene Names: DHODH EC: 1.3.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q02127 (Homo sapiens) Explore Q02127  Go to UniProtKB:  Q02127
PHAROS:  Q02127

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
VGN	D [auth A]	2-ACETAMIDO-5-(4-PHENYLPHENYL)BENZOIC ACID C21 H17 N O3 XXPKIBVYLUEVCV-UHFFFAOYSA-N
DDQ	E [auth A]	DECYLAMINE-N,N-DIMETHYL-N-OXIDE C12 H27 N O ZRKZFNZPJKEWPC-UHFFFAOYSA-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
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
VGN	Binding MOAD:  2WV8	IC50: 210 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.201 
• R-Value Work: 0.185 
• R-Value Observed: 0.185 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.66	α = 90
b = 90.66	β = 90
c = 122.84	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-10-15 
• Released Date: 2010-08-25 
Deposition Author(s): Walse, B., Svensson, B., Fritzson, I., Dahlberg, L., Wellmar, U., Al-Karadaghi, S.

Revision History  

• Version 1.0: 2010-08-25
  Type: Initial release
  
• Version 1.1: 2012-04-25
  Changes: Database references, Version format compliance
• Version 1.2: 2018-01-17
  Changes: Data collection