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: 2.4 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1002/cmdc.200900043

  • 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 thioxoquinaz ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A
A
318Homo sapiensMutation(s): 0 
Gene Names: PDE7A
EC: 3.1.4.53
Find proteins for Q13946 (Homo sapiens)
Go to Gene View: PDE7A
Go to UniProtKB:  Q13946
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
TC8
Query on TC8

Download SDF File 
Download CCD File 
A
3-(2,6-difluorophenyl)-2-(methylthio)quinazolin-4(3H)-one
3-(2,6-difluorophenyl)-2-(methylsulfanyl)quinazolin-4(3H)-one
C15 H10 F2 N2 O S
BFNBJSXMXXQLAW-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TC8IC50: 510 nM BINDINGMOAD
TC8IC50: 510 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.210 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 115.447α = 90.00
b = 115.447β = 90.00
c = 64.389γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
ADSCdata collection
AMoREphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-02-02 
  • Released Date: 2009-04-28 
  • Deposition Author(s): Castano, T., Wang, H.

Revision History 

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance