7CWA

Crystal structure of PDE8A catalytic domain in complex with clofarabine

• PDB DOI: https://doi.org/10.2210/pdb7CWA/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2020-08-27 Released: 2021-09-01 
• Deposition Author(s): Huang, Y., Wu, X.-N., Zhou, Q., Wu, Y., Luo, H.-B.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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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

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

• PubMed: 33291877 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.48 kDa 
• Atom Count: 2,787 
• Modelled Residue Count: 338 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High affinity cAMP-specific and IBMX-insensitive 3',5'-cyclic phosphodiesterase 8A	A	338	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CFB (Subject of Investigation/LOI)	D [auth A]	2-CHLORO-9-(2-DEOXY-2-FLUORO-B -D-ARABINOFURANOSYL)-9H-PURIN-6-AMINE C10 H11 Cl F N5 O3 WDDPHFBMKLOVOX-AYQXTPAHSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 76.261	α = 90
b = 132.246	β = 90
c = 101.916	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-09-01 
Deposition Author(s): Huang, Y., Wu, X.-N., Zhou, Q., Wu, Y., Luo, H.-B.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21877134
National Natural Science Foundation of China (NSFC)	China	81522041

Revision History  

• 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