4PM0

PDE7A catalytic domain in complex with 2-(Cyclopentylamino)thieno[3,2-d]pyrimidin-4(3H)-one derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of 2-(Cyclopentylamino)thieno[3,2-d]pyrimidin-4(3H)-one Derivatives as a New Series of Potent Phosphodiesterase 7 Inhibitors.

Kawai, K.Endo, Y.Asano, T.Amano, S.Sawada, K.Ueo, N.Takahashi, N.Sonoda, Y.Nagai, M.Kamei, N.Nagata, N.

(2014) J.Med.Chem. 57: 9844-9854

  • DOI: 10.1021/jm5008215

  • PubMed Abstract: 
  • The discovery of a new series of potent phosphodiesterase 7 (PDE7) inhibitors is described. Novel thieno[3,2-d]pyrimidin-4(3H)-one hit compounds were identified from our chemical library. Preliminary modifications of the hit compounds were performed, ...

    The discovery of a new series of potent phosphodiesterase 7 (PDE7) inhibitors is described. Novel thieno[3,2-d]pyrimidin-4(3H)-one hit compounds were identified from our chemical library. Preliminary modifications of the hit compounds were performed, resulting in the discovery of a fragment-sized compound (10) with highly improved ligand efficiency. Compound design was guided by structure-activity relationships and computational modeling. The 6-substituted derivatives of the thienopyrimidinone showed diminished activity and enzyme selectivity. However, synthesis of the 7-substituted derivatives resulted in the discovery of 28e, a desirable lead compound that selectively inhibits PDE7 with single-digit nanomolar potency while displaying potent cellular efficacy.


    Organizational Affiliation

    Drug Research Center, Kaken Pharmaceutical Co. Ltd. , 14 Shinomiya Minamigawara-cho, Yamashina, Kyoto 607-8042, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A
A
389Homo 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
32V
Query on 32V

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Download CCD File 
A
2-(cyclopentylamino)-3-ethyl-7-ethynylthieno[3,2-d]pyrimidin-4(3H)-one
C15 H17 N3 O S
OANQHUSHGBNVCN-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 %)
32VIC50: 45 nM (100) BINDINGDB
32VIC50: 45 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.172 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 116.187α = 90.00
b = 116.187β = 90.00
c = 64.458γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2014-12-24
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Data collection, Database references, Derived calculations, Source and taxonomy