9EZ9 | pdb_00009ez9

Crystal structure of human Dihydroorotate Dehydrogenase in complex with the inhibitor N-(3'-(2,2-difluoropropoxy)-2,3,5,6-tetrafluoro-[1,1'-biphenyl]-4-yl)-2-hydroxypyrazolo[1,5-a]pyridine-3-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.233 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9EZ9

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Targeting dihydroorotate dehydrogenase (hDHODH) beyond the barrier: discovery of MEDS700 as blood-brain barrier permeable hDHODH inhibitor.

Sainas, S.Vigato, C.Circosta, P.Zonfrillo, M.Servidei, T.Alberti, M.Rescigno, M.Miggiano, R.Gaidano, V.Vitale, N.Passoni, A.Lanno, A.Buccinna, B.Piccinini, M.Lorenzati, M.Gentile, S.Sferrazza, G.Sgambato, A.Saglio, G.Giorgis, M.Boschi, D.Lolli, M.L.

(2026) Eur J Med Chem 314: 118896-118896

  • DOI: https://doi.org/10.1016/j.ejmech.2026.118896
  • Primary Citation Related Structures: 
    9EZ9

  • PubMed Abstract: 

    Targeting cancer metabolism, particularly de novo nucleotide biosynthesis, has emerged as a promising and innovative therapeutic strategy for both hematologic and solid malignancies, including those of the Central Nervous System (CNS). Glioblastoma cancer stem-like cells are especially vulnerable to pyrimidine synthesis inhibition, highlighting human dihydroorotate dehydrogenase (hDHODH), a rate-limiting enzyme in the de novo pathway, as a potential therapeutic target. MEDS433 is a best-in-class hDHODH inhibitor, that shows efficacy in vivo after oral administration but lacks efficient penetration of the blood-brain barrier (BBB), limiting its utility against CNS tumors. Its lipophilic analogue MEDS613 showed enhanced cellular potency, but its poor metabolic stability and rapid conversion to hydroxylated metabolites precluded its future clinical development. In this study, we aimed to design a novel BBB-permeable hDHODH inhibitor, capable of effectively targeting CNS-localized hDHODH. We began by identifying the metabolic soft spots present in the propyloxy side chain of MEDS613 using this information to develop a metabolically stable analogue, MEDS700 (compound 3, as named in the manuscript), that was shown to inhibit hDHODH in the low nanomolar range (IC 50 hDHODH 1.5 nM). Subsequently, MEDS700 was fully profiled, including detailed analysis of its crystallographic binding mode, pan-antitumor activities in cell-based assays and in vitro cytotoxicity on Peripheral Blood Mononuclear Cells (PBMC). An in vivo pharmacokinetic experiment demonstrated that MEDS700 was able to cross the blood-brain barrier, maintaining therapeutically relevant intracerebral concentrations for up to 24 h after oral administration. Our findings establish MEDS700 as a potent, safe, metabolically stable hDHODH inhibitor, indicating it as a promising candidate for the treatment of hard-to-reach brain tumors.


  • Organizational Affiliation
    • Department of Drug Science and Technology, University of Turin, Via P. Giuria 9, Turin, 10125, Italy; Drug Discovery and Clinic s.r.l., Via Gioacchino Quarello 15/A, Torino, 10135, Italy.

Macromolecule Content 

  • Total Structure Weight: 44.12 kDa 
  • Atom Count: 3,006 
  • Modeled Residue Count: 366 
  • 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
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
A1H8I
(Subject of Investigation/LOI)

Query on A1H8I



Download:Ideal Coordinates CCD File
E [auth A]N-[4-[3-[2,2-bis(fluoranyl)propoxy]phenyl]-2,3,5,6-tetrakis(fluoranyl)phenyl]-2-oxidanyl-pyrazolo[1,5-a]pyridine-3-carboxamide
C23 H15 F6 N3 O3
VMNSFPULVHCEOI-UHFFFAOYSA-N
FMN

Query on FMN



Download:Ideal Coordinates CCD File
C [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
P6G

Query on P6G



Download:Ideal Coordinates CCD File
D [auth A]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-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
F [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.233 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.071α = 90
b = 91.071β = 90
c = 123.441γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministero dell Universita e della RicercaItaly--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-23
    Type: Initial release
  • Version 1.1: 2026-08-12
    Changes: Database references