6OC0 | pdb_00006oc0

Crystal structure of human DHODH with OSU-03012

• PDB DOI: https://doi.org/10.2210/pdb6OC0/pdb

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


• Deposited: 2019-03-21 Released: 2019-11-13 
• Deposition Author(s): Durst, M.A., Lavie, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.184 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Metabolic Modifier Screen Reveals Secondary Targets of Protein Kinase Inhibitors within Nucleotide Metabolism.

Abt, E.R., Rosser, E.W., Durst, M.A., Lok, V., Poddar, S., Le, T.M., Cho, A., Kim, W., Wei, L., Song, J., Capri, J.R., Xu, S., Wu, N., Slavik, R., Jung, M.E., Damoiseaux, R., Czernin, J., Donahue, T.R., Lavie, A., Radu, C.G.

(2020) Cell Chem Biol 27: 197

• PubMed: 31734178 
• DOI: https://doi.org/10.1016/j.chembiol.2019.10.012
• Primary Citation Related Structures: 
  6OC0, 6OC1


• PubMed Abstract: 
  

  Biosynthesis of the pyrimidine nucleotide uridine monophosphate (UMP) is essential for cell proliferation and is achieved by the activity of convergent de novo and salvage metabolic pathways. Here we report the development and application of a cell-based metabolic modifier screening platform that leverages the redundancy in pyrimidine metabolism for the discovery of selective UMP biosynthesis modulators. In evaluating a library of protein kinase inhibitors, we identified multiple compounds that possess nucleotide metabolism modifying activity. The JNK inhibitor JNK-IN-8 was found to potently inhibit nucleoside transport and engage ENT1. The PDK1 inhibitor OSU-03012 (also known as AR-12) and the RAF inhibitor TAK-632 were shown to inhibit the therapeutically relevant de novo pathway enzyme DHODH and their affinities were unambiguously confirmed through in vitro assays and co-crystallization with human DHODH.

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Organizational Affiliation: 
• Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA.
Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA; Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA.
Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA; The Jesse Brown VA Medical Center, Chicago, IL, USA.
Department of Nuclear Medicine, Yonsei University College of Medicine, Seoul, South Korea.
Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA; Department of Surgery, University of California Los Angeles, Los Angeles, CA, USA.
Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA.
Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA, USA.
Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA; Department of Surgery, University of California Los Angeles, Los Angeles, CA, USA; David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA.
Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 41.49 kDa 
• Atom Count: 3,168 
• Modeled Residue Count: 365 
• Deposited Residue Count: 369 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase (quinone), mitochondrial	A	369	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M4J	G [auth A]	N-{4-[5-(phenanthren-2-yl)-3-(trifluoromethyl)-1H-pyrazol-1-yl]phenyl}glycinamide C26 H19 F3 N4 O YULUCECVQOCQFQ-UHFFFAOYSA-N
FMN	C [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
ORO	B [auth A]	OROTIC ACID C5 H4 N2 O4 PXQPEWDEAKTCGB-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.184 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.006	α = 90
b = 91.006	β = 90
c = 123.069	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Coot	model building
MOLREP	phasing
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-11-13 
Deposition Author(s): Durst, M.A., Lavie, A.

Revision History  

• Version 1.0: 2019-11-13
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Database references
• Version 1.2: 2020-03-04
  Changes: Database references
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description