3HDZ

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 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.4 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 

  • DOI: 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 s ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cGMP-specific 3',5'-cyclic phosphodiesterase,cAMP-specific 3',5'-cyclic phosphodiesterase 4A,cGMP-specific 3',5'-cyclic phosphodiesteraseA324Homo sapiensMutation(s): 0 
Gene Names: PDE5APDE5
EC: 3.1.4.35 (PDB Primary Data), 3.1.4.53 (PDB Primary Data)
Find proteins for O76074 (Homo sapiens)
Explore O76074 
Go to UniProtKB:  O76074
NIH Common Fund Data Resources
PHAROS  O76074
Find proteins for P27815 (Homo sapiens)
Explore P27815 
Go to UniProtKB:  P27815
NIH Common Fund Data Resources
PHAROS  P27815
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PD6
Query on PD6

Download CCD File 
A
5-amino-1-butyl-7-phenyl-1,6-naphthyridin-4(1H)-one
C18 H19 N3 O
RLCFNIHFDBMYES-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PD6IC50:  51   nM  Binding MOAD
PD6IC50 :  51   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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