3HDZ | pdb_00003hdz

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.210 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.6 of the entry. See complete history


Literature

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:  
    3HDZ

  • 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.


Macromolecules
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 
Gene Names: PDE5APDE5PDE4ADPDE2
EC: 3.1.4.35 (PDB Primary Data), 3.1.4.53 (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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.210 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
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
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PD6Click on this verticalbar to view details

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