9LO7 | pdb_00009lo7

The crystal structure of PDE4D with 2317b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.293 (Depositor), 0.299 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Structure-Based Optimization of Moracin M as Potent and Selective PDE4 Inhibitors with Antipsoriasis Effects.

Zhang, F.Zheng, T.Wang, X.Chen, Y.Zhang, F.Liu, X.Wang, S.Yang, G.Xie, S.Wu, Q.Xu, C.Zhou, Q.Wu, D.Luo, H.B.Huang, Y.Y.

(2025) J Med Chem 68: 6789-6803

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00266
  • Primary Citation of Related Structures:  
    9LO7

  • PubMed Abstract: 

    Psoriasis is a complex chronic inflammatory disease that severely affects the quality of life of patients. However, current medications could only control the symptoms but not cure psoriasis with unmet medical needs. Herein, structure-based optimizations of natural product moracin M (IC 50 of 2.9 μM) led to a novel PDE4 inhibitor L30 with greatly improved potency (IC 50 of 8.6 nM) and remarkable selectivity across other PDEs families (>201-fold). The binding pattern of L30 with PDE4 revealed by cocrystal structure was different from that of roflumilast. Besides, L30 could effectively inhibit the release of inflammatory cytokines and chemokines in Raw264.7 and HaCaT cell lines. Furthermore, topical administration of L30 exhibited significant therapeutic effects in an imiquimod-induced psoriasis mouse model. These findings highlighted the potential of PDE4 inhibitor L30 as a novel lead for the treatment of psoriasis.


  • Organizational Affiliation
    • Key Laboratory of Tropical Biological Resources of Ministry of Education and Hainan Engineering Research Center for Drug Screening and Evaluation, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3',5'-cyclic-AMP phosphodiesterase 4D
A, B
506Homo 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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EKX (Subject of Investigation/LOI)
Query on A1EKX

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
methyl 4-[[2-[4-[bis(fluoranyl)methoxy]-3-(cyclopropen-1-ylmethoxy)phenyl]-6-oxidanyl-1-benzofuran-7-yl]oxy]-1~{H}-pyrrole-2-carboxylate
C25 H19 F2 N O7
SVBYCXTUMBVJRN-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.293 (Depositor), 0.299 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.348α = 90
b = 79.685β = 90
c = 162.299γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
CrysalisProdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22277019

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Database references