7CWA

Crystal structure of PDE8A catalytic domain in complex with clofarabine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.291 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Rational Design of 2-Chloroadenine Derivatives as Highly Selective Phosphodiesterase 8A Inhibitors.

Huang, Y.Wu, X.N.Zhou, Q.Wu, Y.Zheng, D.Li, Z.Guo, L.Luo, H.B.

(2020) J Med Chem 63: 15852-15863

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01573
  • Primary Citation of Related Structures:  
    7CWA, 7CWF, 7CWG

  • PubMed Abstract: 

    To validate the hypothesis that Tyr748 is a crucial residue to aid the discovery of highly selective phosphodiesterase 8A (PDE8A) inhibitors, we identified a series of 2-chloroadenine derivatives based on the hit clofarabine. Structure-based design targeting Tyr748 in PDE8 resulted in the lead compound 3a (IC 50 = 0.010 μM) with high selectivity with a reasonable druglike profile. In the X-ray crystal structure, 3a bound to PDE8A with a different mode from 3-isobutyl-1-methylxanthine (a pan-PDE inhibitor) and gave a H-bond of 2.7 Å with Tyr748, which possibly interprets the 220-fold selectivity of 3a against PDE2A. Additionally, oral administration of compound 3a achieved remarkable therapeutic effects against vascular dementia (VaD), indicating that PDE8 inhibitors could serve as potential anti-VaD agents.


  • Organizational Affiliation

    School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
High affinity cAMP-specific and IBMX-insensitive 3',5'-cyclic phosphodiesterase 8A338Homo sapiensMutation(s): 0 
Gene Names: PDE8A
EC: 3.1.4.53
UniProt & NIH Common Fund Data Resources
Find proteins for O60658 (Homo sapiens)
Explore O60658 
Go to UniProtKB:  O60658
PHAROS:  O60658
GTEx:  ENSG00000073417 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60658
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.291 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.261α = 90
b = 132.246β = 90
c = 101.916γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21877134
National Natural Science Foundation of China (NSFC)China81522041

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-01
    Type: Initial release
  • Version 1.1: 2022-03-16
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description