8XXS | pdb_00008xxs

Crystal structure of PDE4D catalytic domain complexed with L11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.278 (Depositor), 0.279 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

5-hydroxymethylcytosine features of portal venous blood predict metachronous liver metastases of colorectal cancer and reveal phosphodiesterase 4 as a therapeutic target.

Xu, N.Gao, Z.Wu, D.Chen, H.Zhang, Z.Zhang, L.Wang, Y.Lu, X.Yao, X.Liu, X.Huang, Y.Y.Qiu, M.Wang, S.Liang, J.Mao, C.Zhang, F.Xu, H.Wang, Y.Li, X.Chen, Z.Huang, D.Shi, J.Huang, W.Lei, F.Yang, Z.Chen, L.He, C.Zhu, H.Luo, H.B.Gu, J.Lin, J.

(2025) Clin Transl Med 15: e70189-e70189

  • DOI: https://doi.org/10.1002/ctm2.70189
  • Primary Citation of Related Structures:  
    8XXS

  • PubMed Abstract: 

    Metachronous liver metastases (MLM) are characterised by high incidence and high mortality in clinical colorectal cancer treatment. Currently traditional clinical methods cannot effectively predict and prevent the occurrence of metachronous liver metastasis in colorectal cancer. Based on 5hmC-Seal analysis of blood and tissue samples, this study found that portal venous blood was more relevant to tumour gDNA than peripheral blood. We performed a novel epigenetic liquid biopsy strategy using the 10 5hmC epigenetic alterations, to accurately distinguish MLM patients from patients without metastases. Among these epigenetic alterations, phosphodiesterase 4 (PDE4D) was highly increased in MLM patients and correlated with poor survival. Moreover, our studies demonstrated that PDE4D was a key metastasis-driven target for drug development. Interfering with the function of PDE4D significantly repressed liver metastases. Similarly, roflumilast, a PDE4 inhibitor for chronic obstructive pulmonary disease (COPD) therapy, also inhibits liver metastases. Further studies indicate that blocking the function of PDE4D can affect CRC invasion through the HIF-1α-CCN2 pathway. To develop a more efficient PDE4 inhibitor and reduce the occurrence of adverse events, we also designed several new compounds based on 2-arylbenzofurans and discovered lead L11 with potent affinity for PDE4D and significant suppression of liver metastases. In this work, our study provides a promising strategy for predicting metachronous liver metastasis and discovers L11 as a potential repurposed drug for inhibiting liver metastasis, which have the potential to benefit patients with CRC in the future. KEY POINTS: 5hmC epigenetic markers derived from portal venous blood could accurately predict metachronous metastasis of colorectal cancer. PDE4D was a key metastasis-driven target that promoted metachronous metastasis via the HIF-1α-CCN2 pathway. The newly synthesised compound L11 could specifically inhibit PDE4D and abolish metachronous metastasis of colorectal cancer without obvious toxic side effects.


  • Organizational Affiliation

    Department of Pharmacy, Peking University Third Hospital, Beijing, 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
334Homo 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
A1D5M (Subject of Investigation/LOI)
Query on A1D5M

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
2-[4-[bis(fluoranyl)methoxy]-3-(cyclopropylmethoxy)phenyl]-1-benzofuran-6-ol
C19 H16 F2 O4
ZEGKNTXODOVPOI-UHFFFAOYSA-N
ZN
Query on ZN

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.278 (Depositor), 0.279 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.369α = 90
b = 80.433β = 90
c = 164.585γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1D5MClick on this verticalbar to view details

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: 2025-01-22
    Type: Initial release
  • Version 1.1: 2025-03-12
    Changes: Database references