7Z6C | pdb_00007z6c

Crystal structure of human Dihydroorotate Dehydrogenase in complex with the inhibitor 2-Hydroxy-N-(2-ispropyl-5-methyl-4-phenoxyphenyl)pyrazolo[1,5-a]pyridine-3-carboxamide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.190 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7Z6C

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Targeting Acute Myelogenous Leukemia Using Potent Human Dihydroorotate Dehydrogenase Inhibitors Based on the 2-Hydroxypyrazolo[1,5- a ]pyridine Scaffold: SAR of the Aryloxyaryl Moiety.

Sainas, S.Giorgis, M.Circosta, P.Poli, G.Alberti, M.Passoni, A.Gaidano, V.Pippione, A.C.Vitale, N.Bonanni, D.Rolando, B.Cignetti, A.Ramondetti, C.Lanno, A.Ferraris, D.M.Canepa, B.Buccinna, B.Piccinini, M.Rizzi, M.Saglio, G.Al-Karadaghi, S.Boschi, D.Miggiano, R.Tuccinardi, T.Lolli, M.L.

(2022) J Med Chem 65: 12701-12724

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00496
  • Primary Citation Related Structures: 
    7Z6C

  • PubMed Abstract: 

    In recent years, human dihydroorotate dehydrogenase inhibitors have been associated with acute myelogenous leukemia as well as studied as potent host targeting antivirals. Starting from MEDS433 (IC 50 1.2 nM), we kept improving the structure-activity relationship of this class of compounds characterized by 2-hydroxypyrazolo[1,5- a ]pyridine scaffold. Using an in silico/crystallography supported design, we identified compound 4 (IC 50 7.2 nM), characterized by the presence of a decorated aryloxyaryl moiety that replaced the biphenyl scaffold, with potent inhibition and pro-differentiating abilities on AML THP1 cells (EC 50 74 nM), superior to those of brequinar (EC 50 249 nM) and boosted when in combination with dipyridamole. Finally, compound 4 has an extremely low cytotoxicity on non-AML cells as well as MEDS433; it has shown a significant antileukemic activity in vivo in a xenograft mouse model of AML.


  • Organizational Affiliation
    • Department of Drug Science and Technology, University of Turin, Via P. Giuria 9, Turin 10125, Italy.

Macromolecule Content 

  • Total Structure Weight: 41.08 kDa 
  • Atom Count: 3,128 
  • Modeled Residue Count: 366 
  • Deposited Residue Count: 366 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase (quinone), mitochondrial366Homo 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
IEQ
(Subject of Investigation/LOI)

Query on IEQ



Download:Ideal Coordinates CCD File
D [auth A]~{N}-(5-methyl-4-phenoxy-2-propan-2-yl-phenyl)-2-oxidanyl-pyrazolo[1,5-a]pyridine-3-carboxamide
C24 H23 N3 O3
JABKJLQKEVJGOT-UHFFFAOYSA-N
P6G

Query on P6G



Download:Ideal Coordinates CCD File
E [auth A]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-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
ACT

Query on ACT



Download:Ideal Coordinates CCD File
F [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
IEQ BindingDB:  7Z6C IC50: 7.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.190 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.1α = 90
b = 91.1β = 90
c = 124.03γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Ministry of EducationItalyFAR_2017

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-12
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description