8YTA | pdb_00008yta

The crystal structure of PDE8A with 1604R

• PDB DOI: https://doi.org/10.2210/pdb8YTA/pdb

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


• Deposited: 2024-03-25 Released: 2025-10-22 
• Deposition Author(s): Huang, Y.-Y., Luo, H.-B.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.229 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Targeting phosphodiesterase 8A (PDE8A) to boost adipogenesis and hair cycling

Huang, Y.-Y., Luo, H.-B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42 kDa 
• Atom Count: 2,786 
• Modeled Residue Count: 336 
• Deposited Residue Count: 359 
• 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	359	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
A1D66 (Subject of Investigation/LOI)	D [auth A]	7-[(3-azanyl-5-chloranyl-phenyl)methyl]-8-[3-(4-chlorophenyl)propylsulfanyl]-3-methyl-purine-2,6-dione C22 H21 Cl2 N5 O2 S UPWWHYPFNBVCKJ-UHFFFAOYSA-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: 2.50 Å
• R-Value Free:  0.229 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.182	α = 90
b = 133.184	β = 90
c = 101.468	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
CrysalisPro	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Huang, Y.-Y., Luo, H.-B.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22277019

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release