9VDD | pdb_00009vdd

The crystal structure of PDE4D with inhibitor LH17


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.295 (Depositor), 0.313 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.247 (DCC) 
  • R-Value Observed: 
    0.238 (Depositor) 

Starting Model: experimental
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Literature

Discovery of kaempferol derivatives as novel PDE4 inhibitors for treatment of idiopathic pulmonary fibrosis.

Cao, Y.Liao, X.Huang, P.Lu, R.Wu, Q.Zhong, K.Wang, X.Yang, Y.Liu, X.Fan, J.J.Chen, F.Wang, X.He, X.Luo, H.B.

(2026) Eur J Med Chem 304: 118505-118505

  • DOI: https://doi.org/10.1016/j.ejmech.2025.118505
  • Primary Citation Related Structures: 
    9VDD

  • PubMed Abstract: 

    Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal lung disease with a rapidly rising global incidence. Despite its growing prevalence, effective therapeutic options for IPF remain limited. Phosphodiesterase 4 (PDE4) inhibitors have recently emerged as promising anti-fibrotic candidates. In this study, the natural product kaempferol was identified as a weak PDE4 inhibitor with half maximal inhibitory concentration (IC 50 ) of 22 μM and structure-based optimization by targeting M-pocket was performed, yielding a lead compound LH17 with dramatically improved potency (IC 50 of 73 nM). Crystallographic analysis revealed that this kaempferol-derived compound LH17 displayed distinct interactions with PDE4 M-pocket. Notably, lead LH17 demonstrated remarkable anti-fibrotic efficacy in both in vitro and in vivo models, underscoring its potential as a novel therapeutic agent for IPF treatment. This study also could establish a rational strategy for optimizing weakly bioactive natural PDE4 inhibitors into potent therapeutics.


  • Organizational Affiliation
    • School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China; The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.

Macromolecule Content 

  • Total Structure Weight: 76.54 kDa 
  • Atom Count: 5,370 
  • Modeled Residue Count: 645 
  • Deposited Residue Count: 654 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
3',5'-cyclic-AMP phosphodiesterase 4D
A, B
327Homo 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
A1ERT
(Subject of Investigation/LOI)

Query on A1ERT



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B]
7-methoxy-8-(4-methoxyphenyl)-2,2-dimethyl-5-(pyridin-4-ylmethoxy)pyrano[3,2-g]chromen-6-one
C28 H25 N O6
QBDSTHQLYXBCDP-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: 2.30 Å
  • R-Value Free:  0.295 (Depositor), 0.313 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.247 (DCC) 
  • R-Value Observed: 0.238 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.337α = 90
b = 78.334β = 90
c = 163.16γ = 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: 2026-05-06
    Type: Initial release