7CWA | pdb_00007cwa

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 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.289 (Depositor) 
• R-Value Observed: 
  0.291 (Depositor) 

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 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.
Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, Hainan, 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 
• Modeled 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 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.289 (Depositor) 
• R-Value Observed: 0.291 (Depositor) 

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
• Version 1.3: 2024-11-06
  Changes: Structure summary