6OC0

Crystal structure of human DHODH with OSU-03012


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 

wwPDB Validation   3D Report Full Report

Currently 6OC0 does not have a validation slider image.


This is version 1.3 of the entry. See complete history


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

  • DOI: https://doi.org/10.1016/j.chembiol.2019.10.012
  • Primary Citation of 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.


  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase (quinone), mitochondrial369Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02127
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M4J
Query on M4J

Download Ideal Coordinates CCD File 
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
Query on FMN

Download Ideal Coordinates CCD File 
C [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
ORO
Query on ORO

Download Ideal Coordinates CCD File 
B [auth A]OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.006α = 90
b = 91.006β = 90
c = 123.069γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Cootmodel building
MOLREPphasing
XDSdata scaling

Structure Validation

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Currently 6OC0 does not have a validation slider image.



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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