7VTX | pdb_00007vtx

Crystal structure of PDE8A catalytic domain in complex with 22

• PDB DOI: https://doi.org/10.2210/pdb7VTX/pdb

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


• Deposited: 2021-10-31 Released: 2022-11-02 
• Deposition Author(s): Wu, X.-N., Zhou, Q., Huang, Y.-D., Li, Z., 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: 2.50 Å
• R-Value Free: 
  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.246 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Starting Model: experimental

Literature

Structure-Based Discovery of Orally Efficient PDE8 Inhibitors for the Treatment of Vascular Dementia

Wu, X.-N., Zhou, Q., Huang, Y.-D., Li, Z., Wu, Y., Luo, H.-B.

To be published.

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: 39.6 kDa 
• Atom Count: 2,849 
• 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
80D (Subject of Investigation/LOI)	D [auth A]	2-chloro-9-(3-(2,2-difluoroethoxy)-5-(pyridin-4-yl)benzyl)-9H-purin-6-amine C19 H15 Cl F2 N6 O WQJJOKCRYDFRJI-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.246 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.936	α = 90
b = 132.005	β = 90
c = 101.592	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-02 
Deposition Author(s): Wu, X.-N., Zhou, Q., Huang, Y.-D., Li, Z., 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	22077143

Revision History  

• Version 1.0: 2022-11-02
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary