5OHJ

Human phosphodiesterase 4B catalytic domain in complex with a pyrrolidinyl inhibitor.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Discovery and Optimization of Thiazolidinyl and Pyrrolidinyl Derivatives as Inhaled PDE4 Inhibitors for Respiratory Diseases.

Carzaniga, L., Amari, G., Rizzi, A., Capaldi, C., De Fanti, R., Ghidini, E., Villetti, G., Carnini, C., Moretto, N., Facchinetti, F., Caruso, P., Marchini, G., Battipaglia, L., Patacchini, R., Cenacchi, V., Volta, R., Amadei, F., Pappani, A., Capacchi, S., Bagnacani, V., Delcanale, M., Puccini, P., Catinella, S., Civelli, M., Armani, E.

(2017) J Med Chem 60: 10026-10046

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b01044
  • Primary Citation of Related Structures:  
    5OHJ

  • PubMed Abstract: 

    • Phosphodiesterase 4 (PDE4) is a key cAMP-metabolizing enzyme involved in the pathogenesis of inflammatory disease, and its pharmacological inhibition has been shown to exert therapeutic efficacy in chronic obstructive pulmonary disease (COPD). Herein, we describe a drug discovery program aiming at the identification of novel classes of potent PDE4 inhibitors suitable for pulmonary administration ...

    Phosphodiesterase 4 (PDE4) is a key cAMP-metabolizing enzyme involved in the pathogenesis of inflammatory disease, and its pharmacological inhibition has been shown to exert therapeutic efficacy in chronic obstructive pulmonary disease (COPD). Herein, we describe a drug discovery program aiming at the identification of novel classes of potent PDE4 inhibitors suitable for pulmonary administration. Starting from a previous series of benzoic acid esters, we explored the chemical space in the solvent-exposed region of the enzyme catalytic binding pocket. Extensive structural modifications led to the discovery of a number of heterocycloalkyl esters as potent in vitro PDE4 inhibitors. (S*,S**)-18e and (S*,S**)-22e, in particular, exhibited optimal in vitro ADME and pharmacokinetics properties and dose-dependently counteracted acute lung eosinophilia in an experimental animal model. The optimal biological profile as well as the excellent solid-state properties suggest that both compounds have the potential to be effective topical agents for treating respiratory inflammatory diseases.

    Organizational Affiliation: 

    Chemistry Research and Drug Design, ∥Pharmacology and Toxicology, ‡Pharmacokinetics Biochemistry and Metabolism, †Analytics and Early Formulations, #Project Leader Corporate Drug Development, and ⊥Corporate Pre-Clinical R&D Director, Chiesi Farmaceutici S.p.A , Nuovo Centro Ricerche, Largo Belloli 11/a, 43122 Parma, Italy.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4BA, B421Homo sapiensMutation(s): 0 
Gene Names: PDE4B, DPDE4
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07343
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9VE
Query on 9VE
Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]		[(1~{S})-2-[3,5-bis(chloranyl)-1-oxidanyl-pyridin-1-ium-4-yl]-1-[4-[bis(fluoranyl)methoxy]-3-(cyclopropylmethoxy)phenyl]ethyl] (2~{S})-1-[3-(dimethylcarbamoyl)phenyl]sulfonylpyrrolidine-2-carboxylate
C32 H34 Cl2 F2 N3 O8 S
JHJKKEUBRJUDFY-XCZPVHLTSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
9VE Binding MOAD:  5OHJ IC50: 0.04 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.27α = 90
b = 55.73β = 90
c = 225.56γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2018-01-10
    Changes: Database references
  • Version 1.2: 2019-04-03
    Changes: Data collection, Source and taxonomy