8OEG

PDE4B bound to MAPI compound 92a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Optimization of M 3 Antagonist-PDE4 Inhibitor (MAPI) Dual Pharmacology Molecules for the Treatment of COPD.

Rizzi, A.Amari, G.Pivetti, F.Delcanale, M.Amadei, F.Pappani, A.Fornasari, L.Villetti, G.Marchini, G.Pisano, A.R.Pitozzi, V.Pittelli, M.G.Trevisani, M.Salvadori, M.Cenacchi, V.Fioni, A.Puccini, P.Civelli, M.Patacchini, R.Baker-Glenn, C.Van de Poel, H.Blackaby, W.Nash, K.Armani, E.

(2023) J Med Chem 66: 11476-11497

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01012
  • Primary Citation of Related Structures:  
    8OEG

  • PubMed Abstract: 

    Aiming at the inhaled treatment of pulmonary diseases, the optimization process of the previously reported MAPI compound 92a is herein described. The project was focused on overcoming the chemical stability issue and achieving a balanced bronchodilator/anti-inflammatory profile in rats in order to be confident in a clinical effect without having to overdose at one of the biological targets. The chemical strategy was based on fine-tuning of the substitution pattern in the muscarinic and PDE4 structural portions of the dual pharmacology compounds, also making use of the analysis of a proprietary crystal structure in the PDE4 catalytic site. Compound 10f was identified as a chemically stable, potent, and in vivo balanced MAPI lead compound, as assessed in bronchoconstriction and inflammation assays in rats after intratracheal administration. After the in-depth investigation of the pharmacological and solid-state profile, 10f proved to be safe and suitable for development.


  • Organizational Affiliation

    Chiesi Farmaceutici S.p.A., Centro Ricerche, Largo Belloli 11/a, 43122 Parma, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4B421Homo sapiensMutation(s): 0 
Gene Names: PDE4BDPDE4
EC: 3.1.4.53
UniProt & NIH Common Fund Data Resources
Find proteins for Q07343 (Homo sapiens)
Explore Q07343 
Go to UniProtKB:  Q07343
PHAROS:  Q07343
GTEx:  ENSG00000184588 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07343
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VL9 (Subject of Investigation/LOI)
Query on VL9

Download Ideal Coordinates CCD File 
D [auth A][(1~{S})-2-[3,5-bis(chloranyl)-1-oxidanyl-pyridin-4-yl]-1-(3,4-dimethoxyphenyl)ethyl] 5-[[[(1~{R})-2-[[(3~{R})-1-azabicyclo[2.2.2]octan-3-yl]oxy]-2-oxidanylidene-1-phenyl-ethyl]amino]methyl]thiophene-2-carboxylate
C36 H38 Cl2 N3 O7 S
IMHXWUGXDHLPGY-LEEDBYTESA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.76α = 90
b = 95.76β = 90
c = 85.46γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
autoPROCdata processing
xia2data reduction
XDSdata reduction
pointlessdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-08
    Changes: Database references