7CA1

Crystal structure of dihydroorotase in complex with plumbagin from Saccharomyces cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Plumbagin, a Natural Product with Potent Anticancer Activities, Binds to and Inhibits Dihydroorotase, a Key Enzyme in Pyrimidine Biosynthesis.

Guan, H.H.Huang, Y.H.Lin, E.S.Chen, C.J.Huang, C.Y.

(2021) Int J Mol Sci 22

  • DOI: https://doi.org/10.3390/ijms22136861
  • Primary Citation of Related Structures:  
    7CA1

  • PubMed Abstract: 

    Dihydroorotase (DHOase) is the third enzyme in the de novo biosynthesis pathway for pyrimidine nucleotides, and an attractive target for potential anticancer chemotherapy. By screening plant extracts and performing GC-MS analysis, we identified and characterized that the potent anticancer drug plumbagin (PLU), isolated from the carnivorous plant Nepenthes miranda , was a competitive inhibitor of DHOase. We also solved the complexed crystal structure of yeast DHOase with PLU (PDB entry 7CA1), to determine the binding interactions and investigate the binding modes. Mutational and structural analyses indicated the binding of PLU to DHOase through loop-in mode, and this dynamic loop may serve as a drug target. PLU exhibited cytotoxicity on the survival, migration, and proliferation of 4T1 cells and induced apoptosis. These results provide structural insights that may facilitate the development of new inhibitors targeting DHOase, for further clinical anticancer chemotherapies.


  • Organizational Affiliation

    Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DihydroorotaseA,
B [auth C],
C [auth B],
D
372Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: URA4YLR420WL9931.1
EC: 3.5.2.3
UniProt
Find proteins for P20051 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20051 
Go to UniProtKB:  P20051
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20051
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
90R (Subject of Investigation/LOI)
Query on 90R

Download Ideal Coordinates CCD File 
H [auth C],
N [auth D]
5-hydroxy-2-methylnaphthalene-1,4-dione
C11 H8 O3
VCMMXZQDRFWYSE-UHFFFAOYSA-N
LMR
Query on LMR

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B]
(2S)-2-hydroxybutanedioic acid
C4 H6 O5
BJEPYKJPYRNKOW-REOHCLBHSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
I [auth C]
J [auth C]
L [auth B]
F [auth A],
G [auth A],
I [auth C],
J [auth C],
L [auth B],
M [auth B],
O [auth D],
P [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A,
B [auth C],
C [auth B],
D
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.24α = 90
b = 88.36β = 95.16
c = 103.42γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)Taiwan--

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-09
    Type: Initial release
  • Version 1.1: 2021-07-14
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description