9S1I | pdb_00009s1i

Crystal structure of human Dihydroorotate Dehydrogenase in complex with arzanol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 
    0.175 (Depositor), 0.176 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Arzanol Inhibits Human Dihydroorotate Dehydrogenase and Shows Antiviral Activity.

Alberti, M.Tamburello, M.Salamone, S.Gallinella, G.Sanna, C.Appendino, G.B.Lolli, M.L.Massarotti, A.Pollastro, F.Miggiano, R.

(2025) J Nat Prod 88: 2586-2595

  • DOI: https://doi.org/10.1021/acs.jnatprod.5c00887
  • Primary Citation Related Structures: 
    9S1I

  • PubMed Abstract: 

    Human dihydroorotate dehydrogenase ( h DHODH), catalyzing the rate-limiting step of the pyrimidine biosynthesis pathway (PBP), is a drug target extensively investigated for various diseases including cancer, autoimmune disorders, and viral infections. We present evidence that the heterodimeric phloroglucinylpyrone arzanol potently inhibits h DHODH by competing with ubiquinone for binding to the lipophilic patch (LP) of the enzyme. Co-crystallization experiments on the enzyme-arzanol complex provided further insights into the binding pocket of h DHODH, revealing detailed features that could inspire the design of innovative inhibitors. The cellular translation of these enzymatic and biochemical data was validated in antiviral assays on SARS-CoV-2 infected cells. Taken together, these results exemplify the potential of natural products to explore novel areas of the protein druggable space and provide information relevant to multiple critical areas of drug discovery.


  • Organizational Affiliation
    • Department of Pharmaceutical Sciences, University of Piemonte Orientale, Via G. Bovio 6, 28100 Novara, Italy.

Macromolecule Content 

  • Total Structure Weight: 43.9 kDa 
  • Atom Count: 3,083 
  • Modeled Residue Count: 350 
  • Deposited Residue Count: 390 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase (quinone), mitochondrial390Homo 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
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
(Subject of Investigation/LOI)

Query on FMN



Download:Ideal Coordinates CCD File
B [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
A1JKW
(Subject of Investigation/LOI)

Query on A1JKW



Download:Ideal Coordinates CCD File
D [auth A]3-[[3-ethanoyl-5-(3-methylbut-2-enyl)-2,4,6-tris(oxidanyl)phenyl]methyl]-6-ethyl-5-methyl-4-oxidanyl-pyran-2-one
C22 H26 O7
ZOIAPLVBZQQHCG-UHFFFAOYSA-N
ORO
(Subject of Investigation/LOI)

Query on ORO



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

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ACT

Query on ACT



Download:Ideal Coordinates CCD File
E [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free:  0.175 (Depositor), 0.176 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.477α = 90
b = 90.477β = 90
c = 122.86γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministero dell Universita e della RicercaItalyP2022P8KMF

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Database references