8ZQ2 | pdb_00008zq2

The crystal structure of PDE4D with isoaurostatin derivatives 2-1

• PDB DOI: https://doi.org/10.2210/pdb8ZQ2/pdb

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


• Deposited: 2024-05-31 Released: 2025-02-12 
• Deposition Author(s): Huang, Y.-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: 2.10 Å
• R-Value Free: 
  0.251 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Structure-based optimization of isoaurostatin as novel PDE4 inhibitors with anti-fibrotic effects

Huang, Y.Y., Luo, X., Zhang, K., Liang, Y., Zhang, F., Liao, G., Xie, S., Huang, P.L., Hou, S., Zhou, Q., Zou, Y., Luo, H.B.

(2024) Chin Chem Lett : 110586

• DOI: https://doi.org/10.1016/j.cclet.2024.110586

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 116.32 kDa 
• Atom Count: 5,507 
• Modeled Residue Count: 648 
• Deposited Residue Count: 1,012 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3',5'-cyclic-AMP phosphodiesterase 4D	A, B	506	Homo sapiens	Mutation(s): 0  Gene Names: PDE4D, DPDE3 EC: 3.1.4.53
UniProt & NIH Common Fund Data Resources
Find proteins for Q08499 (Homo sapiens) Explore Q08499  Go to UniProtKB:  Q08499
PHAROS:  Q08499 GTEx:  ENSG00000113448

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D8O (Subject of Investigation/LOI)	E [auth A], H [auth B]	(3~{Z})-3-[(3-ethoxy-4-methoxy-phenyl)methylidene]-6-oxidanyl-1-benzofuran-2-one C18 H16 O5 HEJMHLCXAFJBCY-ZSOIEALJSA-N
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.251 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.188	α = 90
b = 80.167	β = 90
c = 162.82	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
CrysalisPro	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Huang, Y.-Y., Luo, H.-B.

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

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release
  
• Version 1.1: 2025-09-03
  Changes: Structure summary