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 9XC5 | pdb_00009xc5

Crystal structure of PDE5A in complex with a flavonoid glycoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 
    0.234 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9XC5

This is version 1.0 of the entry. See complete history. 

Literature

Mechanistic study of PDE5A inhibitors from the prepared folium of Epimedium sagittatum maxim.

Fang, Y., Wu, S., Xu, J., Chen, J., Shi, W., Wang, H., Li, S., Xie, H., Tao, H., Pan, L., Zang, Y., Yao, G., Zheng, X.

(2026) J Struct Biol 218: 108279-108279

  • DOI: https://doi.org/10.1016/j.jsb.2025.108279
  • Primary Citation Related Structures: 
    9XC4, 9XC5

  • PubMed Abstract: 

    Phosphodiesterase-5 (PDE5A) is a critical therapeutic target for treating male erectile dysfunction (ED). PDE5A inhibitors like sildenafil are clinically effective, but exhibit side effects due to non-specific inhibition of related PDE isoforms. This necessitates the discovery of safer and specific PDE5A inhibitors. The prepared folium of Epimedium sagittatum (PFES) is a primary sovereign drug in traditional Chinese medicine (TCM) formulations for ED. As part of ongoing research into its pharmacodynamic basis, this study isolated and identified forty-four flavonoids and organic acids from PFES. The inhibitory activities of these compounds against PDE5A were systematically evaluated, and three compounds (1, 5, and 6) are demonstrated to have significant PDE5A inhibition activities. Notably, the compound 6 (baohuoside I), was previously confirmed the activitywith PDE5A, and its co-crystal structure with PDE5A was also reported. To elucidate the molecular mechanisms underlying the inhibition of PDE5A by compound 1 and 5, we solved the crystal structures of the catalytic domain of PDE5A in complex with compound 1 and 5. Further structural analyses revealed distinct binding modes adopted by 1 and 5 for occupying the PDE5A active site, highlighting their specific interactions with PDE5A compared to each other and to other established inhibitors like sildenafil. In summary, these findings underscore the potential of PFES-derived natural compounds as specific PDE5A inhibitors, and provide crucial insights for the rational development of novel ED therapeutics with potentially improved specificity and reduced side effects based on TCM constituents.


  • Organizational Affiliation: 
    • State Key Laboratory of Discovery and Utilization of Functional Components in Traditional Chinese Medicine, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, PR China.

Macromolecule Content 

  • Total Structure Weight: 38.63 kDa 
  • Atom Count: 2,387 
  • Modeled Residue Count: 290 
  • Deposited Residue Count: 326 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
cGMP-specific 3',5'-cyclic phosphodiesterase326Homo sapiensMutation(s): 0 
Gene Names: PDE5A, PDE5
EC: 3.1.4.35
UniProt & NIH Common Fund Data Resources
Find proteins for O76074 (Homo sapiens)
Explore O76074 
Go to UniProtKB:  O76074
PHAROS:  O76074
GTEx:  ENSG00000138735 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76074
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-L-rhamnopyranose-(1-2)-alpha-L-rhamnopyranose-(1-6)-3,5,7-trihydroxy-2-(4-methoxyphenyl)-8-(3-methylbutyl)-4H-chromen-4-oneB [auth D]3N/AN/A

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free:  0.234 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.465α = 90
b = 74.465β = 90
c = 131.907γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
autoPROCdata reduction
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-10-14
    Type: Initial release