6VND

Quaternary Complex of human dihydroorotate dehydrogenase (DHODH) with flavin mononucleotide (FMN), orotic acid and AG-636

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report

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This is version 1.2 of the entry. See complete history. 


Literature

Selective Vulnerability to Pyrimidine Starvation in Hematologic Malignancies Revealed by AG-636, a Novel Clinical-Stage Inhibitor of Dihydroorotate Dehydrogenase.

McDonald, G., Chubukov, V., Coco, J., Truskowski, K., Narayanaswamy, R., Choe, S., Steadman, M., Artin, E., Padyana, A.K., Jin, L., Ronseaux, S., Locuson, C., Fan, Z.P., Erdmann, T., Mann, A., Hayes, S., Fletcher, M., Nellore, K., Rao, S.S., Subramanya, H., Reddy, K.S., Panigrahi, S.K., Antony, T., Gopinath, S., Sui, Z., Nagaraja, N., Dang, L., Lenz, G., Hurov, J., Biller, S.A., Murtie, J., Marks, K.M., Ulanet, D.B.

(2020) Mol Cancer Ther 19: 2502-2515

  • DOI: https://doi.org/10.1158/1535-7163.MCT-20-0550
  • Primary Citation of Related Structures:  
    6VND

  • PubMed Abstract: 

    Agents targeting metabolic pathways form the backbone of standard oncology treatments, though a better understanding of differential metabolic dependencies could instruct more rationale-based therapeutic approaches. We performed a chemical biology screen that revealed a strong enrichment in sensitivity to a novel dihydroorotate dehydrogenase (DHODH) inhibitor, AG-636, in cancer cell lines of hematologic versus solid tumor origin. Differential AG-636 activity translated to the in vivo setting, with complete tumor regression observed in a lymphoma model. Dissection of the relationship between uridine availability and response to AG-636 revealed a divergent ability of lymphoma and solid tumor cell lines to survive and grow in the setting of depleted extracellular uridine and DHODH inhibition. Metabolic characterization paired with unbiased functional genomic and proteomic screens pointed to adaptive mechanisms to cope with nucleotide stress as contributing to response to AG-636. These findings support targeting of DHODH in lymphoma and other hematologic malignancies and suggest combination strategies aimed at interfering with DNA-damage response pathways.

    • Organizational Affiliation: 

    Agios Pharmaceuticals, Inc., Cambridge, Massachusetts. dulanet@reparerx.com Gabrielle.McDonald@agios.com.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase (quinone), mitochondrial368Homo 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 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN
Download Ideal Coordinates CCD File 
K [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
R4P (Subject of Investigation/LOI)
Query on R4P
Download Ideal Coordinates CCD File 
B [auth A]1-methyl-5-(2'-methyl[1,1'-biphenyl]-4-yl)-1H-benzotriazole-7-carboxylic acid
C21 H17 N3 O2
GSBZRCGZLMBSNY-UHFFFAOYSA-N
DET
Query on DET
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		UNDECYLAMINE-N,N-DIMETHYL-N-OXIDE
C13 H29 N O
OZHBUVQCJMARBN-UHFFFAOYSA-N
DDQ
Query on DDQ
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]		DECYLAMINE-N,N-DIMETHYL-N-OXIDE
C12 H27 N O
ZRKZFNZPJKEWPC-UHFFFAOYSA-N
ORO
Query on ORO
Download Ideal Coordinates CCD File 
L [auth A]OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N
GOL
Query on GOL
Download Ideal Coordinates CCD File 
P [auth A]
Q [auth A]
R [auth A]
S [auth A]
T [auth A]
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT
Download Ideal Coordinates CCD File 
M [auth A],
N [auth A],
O [auth A]		ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL
Download Ideal Coordinates CCD File 
G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA
Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
R4P Binding MOAD:  6VND IC50: 17 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.526α = 90
b = 90.526β = 90
c = 123.761γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2020-12-16
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Advisory, Data collection, Database references, Refinement description