3U2O | pdb_00003u2o

Dihydroorotate Dehydrogenase (DHODH) crystal structure in complex with small molecule inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3U2O/pdb

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


• Deposited: 2011-10-04 Released: 2011-11-16 
• Deposition Author(s): Lozoya, E., Segarra, V., Erra, M., Wenzkowski, C., Jestel, A., Krapp, S., Blaesse, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.205 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Biaryl analogues of teriflunomide as potent DHODH inhibitors.

Erra, M., Moreno, I., Sanahuja, J., Andres, M., Reinoso, R.F., Lozoya, E., Pizcueta, P., Godessart, N., Castro-Palomino, J.C.

(2011) Bioorg Med Chem Lett 21: 7268-7272

• PubMed: 22078215 
• DOI: https://doi.org/10.1016/j.bmcl.2011.10.052
• Primary Citation Related Structures: 
  3U2O


• PubMed Abstract: 
  

  The structure-activity relationships of a novel series of biaryl dihydroorotate dehydrogenase (DHODH) inhibitors related to teriflunomide are disclosed. These biaryl derivatives were the result of structure-based design and proved to be potent DHODH inhibitors which in addition showed good antiproliferative activities on peripheral blood mononuclear cells and good efficacies in vivo in the rat adjuvant-induced-arthritis model.

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Organizational Affiliation: 
• Almirall, R&D Centre, Laureà Miró 408-410, Sant Feliu de Llobregat, 08980 Barcelona, Spain. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 44.28 kDa 
• Atom Count: 3,198 
• Modeled Residue Count: 366 
• Deposited Residue Count: 395 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase (quinone), mitochondrial	A	395	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 GTEx:  ENSG00000102967

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
03U	D [auth A]	methyl 4-{[(2Z)-2-cyano-3-hydroxypent-2-enoyl]amino}-4'-fluorobiphenyl-2-carboxylate C20 H17 F N2 O4 IYKUBGQVTQQVJG-ZCXUNETKSA-N
ORO	C [auth A]	OROTIC ACID C5 H4 N2 O4 PXQPEWDEAKTCGB-UHFFFAOYSA-N
SO4	H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	E [auth A], F [auth A], G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.205 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.028	α = 90
b = 91.028	β = 90
c = 122.465	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-16 
Deposition Author(s): Lozoya, E., Segarra, V., Erra, M., Wenzkowski, C., Jestel, A., Krapp, S., Blaesse, M.

Revision History  

• Version 1.0: 2011-11-16
  Type: Initial release
  
• Version 1.1: 2012-09-05
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description