8WDN

Crystal structure of PDE4D complexed with 7b-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

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Ligand Structure Quality Assessment 


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Literature

Identification of Dihydrobenzofuran Neolignans as Novel PDE4 Inhibitors and Evaluation of Antiatopic Dermatitis Efficacy in DNCB-Induced Mice Model.

Gu, C.Liu, J.Qian, F.Yu, W.Huang, D.Shen, J.Feng, C.Chen, K.Li, Y.Jiang, X.Xu, Y.Zhang, L.

(2024) J Med Chem 67: 4855-4869

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c02424
  • Primary Citation of Related Structures:  
    8WDN, 8WDO

  • PubMed Abstract: 

    Atopic dermatitis is a chronic relapsing skin disease characterized by recurrent, pruritic, localized eczema, while PDE4 inhibitors have been reported to be effective as antiatopic dermatitis agents. 3',4- O -dimethylcedrusin (DCN) is a natural dihydrobenzofuran neolignan isolated from Magnolia biondii with moderate potency against PDE4 (IC 50 = 3.26 ± 0.28 μM) and a binding mode similar to that of apremilast, an approved PDE4 inhibitor for the treatment of psoriasis. The structure-based optimization of DCN led to the identification of 7b-1 that showed high inhibitory potency on PDE4 (IC 50 = 0.17 ± 0.02 μM), good anti-TNF-α activity (EC 50 = 0.19 ± 0.10 μM), remarkable selectivity profile, and good skin permeability. The topical treatment of 7b-1 resulted in the significant benefits of pharmacological intervention in a DNCB-induced atopic dermatitis-like mice model, demonstrating its potential for the development of novel antiatopic dermatitis agents.


  • Organizational Affiliation

    School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4D
A, B
349Homo sapiensMutation(s): 0 
Gene Names: PDE4DDPDE3
EC: 3.1.4.53
UniProt & NIH Common Fund Data Resources
Find proteins for Q08499 (Homo sapiens)
Explore Q08499 
Go to UniProtKB:  Q08499
PHAROS:  Q08499
GTEx:  ENSG00000113448 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08499
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
W8E (Subject of Investigation/LOI)
Query on W8E

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
3-[(2~{S},3~{R})-7-ethoxy-2-(3-ethoxy-4-methoxy-phenyl)-3-(hydroxymethyl)-2,3-dihydro-1-benzofuran-5-yl]propan-1-ol
C23 H30 O6
NWARZTAQZRDFKR-PGRDOPGGSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
K [auth B],
L [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.965α = 90
b = 80.407β = 90
c = 163.413γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
SCALAdata scaling

Structure Validation

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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: 2024-08-28
    Type: Initial release