4PM0 | pdb_00004pm0

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: 2.10 Å
  • R-Value Free: 
    0.218 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/10.1021/jm5008215
  • Primary Citation Related Structures: 
    4PM0

  • 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, 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.

Macromolecule Content 

  • Total Structure Weight: 44.88 kDa 
  • Atom Count: 2,855 
  • Modeled Residue Count: 318 
  • Deposited Residue Count: 389 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A389Homo sapiensMutation(s): 0 
Gene Names: PDE7A
EC: 3.1.4.53
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
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Reference Sequence

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
32V BindingDB:  4PM0 IC50: 45 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.218 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.187α = 90
b = 116.187β = 90
c = 64.458γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2014-12-24
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description