Identification, Synthesis, and SAR of Amino Substituted Pyrido[3,2b]pryaziones as Potent and Selective PDE5 Inhibitors

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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Identification, synthesis and SAR of amino substituted pyrido[3,2b]pyrazinones as potent and selective PDE5 inhibitors.

Owen, D.R.Walker, J.K.Jon Jacobsen, E.Freskos, J.N.Hughes, R.O.Brown, D.L.Bell, A.S.Brown, D.G.Phillips, C.Mischke, B.V.Molyneaux, J.M.Fobian, Y.M.Heasley, S.E.Moon, J.B.Stallings, W.C.Joseph Rogier, D.Fox, D.N.Palmer, M.J.Ringer, T.Rodriquez-Lens, M.Cubbage, J.W.Blevis-Bal, R.M.Benson, A.G.Acker, B.A.Maddux, T.M.Tollefson, M.B.Bond, B.R.Macinnes, A.Yu, Y.

(2009) Bioorg Med Chem Lett 19: 4088-4091

  • DOI: https://doi.org/10.1016/j.bmcl.2009.06.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A new class of potent and selective PDE5 inhibitors is disclosed. Guided by X-ray crystallographic data, optimization of an HTS lead led to the discovery of a series of 2-aryl, (N8)-alkyl substituted-6-aminosubstituted pyrido[3,2b]pyrazinones which show potent inhibition of the PDE5 enzyme. Synthetic details and some structure-activity relationships are also presented.

  • Organizational Affiliation

    Department of Chemistry, Pfizer Global Research and Development, Ramsgate Road, Sandwich, Kent CT13 9NJ, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cGMP-specific 3',5'-cyclic phosphodiesterase,cAMP-specific 3',5'-cyclic phosphodiesterase 4A,cGMP-specific 3',5'-cyclic phosphodiesterase324Homo sapiensMutation(s): 0 
EC: (PDB Primary Data), (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O76074 (Homo sapiens)
Explore O76074 
Go to UniProtKB:  O76074
PHAROS:  O76074
GTEx:  ENSG00000138735 
Find proteins for P27815 (Homo sapiens)
Explore P27815 
Go to UniProtKB:  P27815
PHAROS:  P27815
GTEx:  ENSG00000065989 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP27815O76074
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
PD6 Binding MOAD:  3HDZ IC50: 51 (nM) from 1 assay(s)
PDBBind:  3HDZ IC50: 51 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.015α = 90
b = 76.502β = 102.9
c = 80.72γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-06-21
    Changes: Advisory, Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2018-04-04
    Changes: Data collection
  • Version 1.5: 2023-07-26
    Changes: Database references, Derived calculations
  • Version 1.6: 2024-05-22
    Changes: Data collection