2CHM

Crystal structure of N2 substituted pyrazolo pyrimidinones - a flipped binding mode in PDE5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Novel Series of Potent and Selective Pde5 Inhibitors with Potential for High and Dose-Independent Oral Bioavailability

Allerton, C.M.N.Barber, C.G.Beaumont, K.C.Brown, D.G.Cole, S.M.Ellis, D.Lane, C.A.L.Maw, G.N.Mount, N.M.Rawson, D.J.Robinson, C.M.Street, S.D.A.Summerhill, N.W.

(2006) J.Med.Chem. 49: 3581

  • DOI: 10.1021/jm060113e

  • PubMed Abstract: 
  • Sildenafil (5-[2-ethoxy-5-(4-methyl-1-piperazinylsulfonyl)phenyl]-1-methyl-3-n-propyl-1,6-dihydro-7H-pyrazolo[4,3-d]pyrimidin-7-one), a potent and selective phosphodiesterase type 5 (PDE5) inhibitor, provided the first oral treatment for male erectil ...

    Sildenafil (5-[2-ethoxy-5-(4-methyl-1-piperazinylsulfonyl)phenyl]-1-methyl-3-n-propyl-1,6-dihydro-7H-pyrazolo[4,3-d]pyrimidin-7-one), a potent and selective phosphodiesterase type 5 (PDE5) inhibitor, provided the first oral treatment for male erectile dysfunction. The objective of the work reported in this paper was to combine high levels of PDE5 potency and selectivity with high and dose-independent oral bioavailability, to minimize the impact on the C(max) of any interactions with coadministered drugs in the clinic. This goal was achieved through identification of a lower clearance series with a high absorption profile, by replacing the 5'-piperazine sulfonamide in the sildenafil template with a 5'-methyl ketone. This novel series provided compounds with low metabolism in human hepatocytes, excellent caco-2 flux, and the potential for good aqueous solubility. The in vivo oral and iv pharmacokinetic profiles of example compounds confirmed the high oral bioavailability predicted from these in vitro screens. 5-(5-Acetyl-2-butoxy-3-pyridinyl)-3-ethyl-2-(1-ethyl-3-azetidinyl)-2,6-dihydro-7H-pyrazolo[4,3-d]pyrimidin-7-one (2) was selected for progression into the clinic.


    Organizational Affiliation

    Discovery Chemistry, Lead Discovery, and Discovery Biology, Pfizer Global Research & Development, Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom. charlotte.allerton@pfizer.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CGMP-SPECIFIC 3', 5'-CYCLIC PHOSPHODIESTERASE, CAMP-SPECIFIC 3', 5'-CYCLIC PHOSPHODIESTERASE 4B
A
326Homo sapiensGene Names: PDE4B (DPDE4), PDE5A (PDE5)
EC: 3.1.4.53 3.1.4.35
Find proteins for Q07343 (Homo sapiens)
Go to Gene View: PDE4B
Go to UniProtKB:  Q07343
Find proteins for O76074 (Homo sapiens)
Go to Gene View: PDE5A
Go to UniProtKB:  O76074
Small Molecules
Ligands 4 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
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
3P4
Query on 3P4

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Download CCD File 
A
5-[2-(BUT-3-EN-1-YLOXY)-5-(1-HYDROXYVINYL)PYRIDIN-3-YL]-3-ETHYL-2-(1-ETHYLAZETIDIN-3-YL)-1,2,6,7A-TETRAHYDRO-7H-PYRAZOLO[4,3-D]PYRIMIDIN-7-ONE
5-(5-ACETYL-2-BUTOXY-3-PYRIDINYL)-3-ETHYL-2-(1-ETHYL-3-AZETIDINYL)-2,6-DIHYDRO-7H-PYRAZOLO (4,3-D) PYRIMIDIN-7-ONE
C23 H29 N6 O3
XQNNCUVRTZCFFZ-UHFFFAOYSA-O
 Ligand Interaction
MES
Query on MES

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Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3P4IC50: 5.5 nM BINDINGMOAD
3P4IC50: 5.5 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 55.836α = 90.00
b = 76.656β = 102.58
c = 81.269γ = 90.00
Software Package:
Software NamePurpose
CNXphasing
DENZOdata reduction
CNXrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance