3G3N

PDE7A catalytic domain in complex with 3-(2,6-difluorophenyl)-2-(methylthio)quinazolin-4(3H)-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Synthesis, structural analysis, and biological evaluation of thioxoquinazoline derivatives as phosphodiesterase 7 inhibitors

Castano, T.Wang, H.Campillo, N.E.Ballester, S.Gonzalez-Garcia, C.Hernandez, J.Perez, C.Cuenca, J.Perez-Castillo, A.Martinez, A.Huertas, O.Gelpi, J.L.Luque, F.J.Ke, H.Gil, C.

(2009) ChemMedChem 4: 866-876

  • DOI: https://doi.org/10.1002/cmdc.200900043
  • Primary Citation of Related Structures:  
    3G3N

  • PubMed Abstract: 

    PDE7 inhibitors regulate pro-inflammatory and immune T-cell functions, and are a potentially novel class of drugs especially useful in the treatment of a wide variety of immune and inflammatory disorders. Starting from our lead family of thioxoquinazolines, we designed, synthesized, and characterized a novel series of thioxoquinazoline derivatives. Many of these compounds showed inhibitory potencies at sub-micromolar levels against the catalytic domain of PDE7A1 and at the micromolar level against PDE4D2. Cell-based studies showed that these compounds not only increased intracellular cAMP levels, but also had interesting anti-inflammatory properties within a therapeutic window. The in silico data predict that these compounds are capable of the crossing the blood-brain barrier. The X-ray crystal structure of the PDE7A1 catalytic domain in complex with compound 15 at a resolution of 2.4 A demonstrated that hydrophobic interactions at the active site pocket are a key feature. This structure, together with molecular modeling, provides insight into the selectivity of the PDE inhibitors and a template for the discovery of new PDE7 or PDE7/PDE4 dual inhibitors.


  • Organizational Affiliation

    Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A318Homo sapiensMutation(s): 0 
Gene Names: PDE7APDE7A1
EC: 3.1.4.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q13946 (Homo sapiens)
Explore Q13946 
Go to UniProtKB:  Q13946
PHAROS:  Q13946
GTEx:  ENSG00000205268 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13946
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
TC8 PDBBind:  3G3N IC50: 510 (nM) from 1 assay(s)
Binding MOAD:  3G3N IC50: 510 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.447α = 90
b = 115.447β = 90
c = 64.389γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations