7F0I

phosphodiesterase-9A in complex with inhibitor 4b

• PDB DOI: https://doi.org/10.2210/pdb7F0I/pdb

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


• Deposited: 2021-06-04 Released: 2022-04-13 
• Deposition Author(s): Wu, Y., 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: 2.70 Å
• R-Value Free: 0.334 
• R-Value Work: 0.271 
• R-Value Observed: 0.274 

Literature

Discovery of Potent Phosphodiesterase-9 Inhibitors for the Treatment of Hepatic Fibrosis

Wu, Y., Wang, Q., Jiang, M.Y., Huang, Y.Y., Zhu, Z., Han, C., Tian, Y.J., Zhang, B., Luo, H.B.

(2021) J Med Chem 64: 9537-9549

• DOI: https://doi.org/10.1021/acs.jmedchem.1c00862

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 124.53 kDa 
• Atom Count: 5,368 
• Modelled Residue Count: 630 
• Deposited Residue Count: 1,066 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform PDE9A2 of High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	A, B	533	Homo sapiens	Mutation(s): 0  Gene Names: PDE9A EC: 3.1.4.35
UniProt & NIH Common Fund Data Resources
Find proteins for O76083 (Homo sapiens) Explore O76083  Go to UniProtKB:  O76083
PHAROS:  O76083 GTEx:  ENSG00000160191

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
06A (Subject of Investigation/LOI)	E [auth A], H [auth B]	1-cyclopentyl-6-[[(2R)-1-(6-fluoranyl-2-azaspiro[3.3]heptan-2-yl)-1-oxidanylidene-propan-2-yl]amino]-5H-pyrazolo[3,4-d]pyrimidin-4-one C19 H25 F N6 O2 GJXGHHNPNGRGBH-LLVKDONJSA-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: 2.70 Å
• R-Value Free: 0.334 
• R-Value Work: 0.271 
• R-Value Observed: 0.274 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.467	α = 90
b = 103.467	β = 90
c = 268.921	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-04-13 
Deposition Author(s): Wu, Y., Huang, Y.Y., Luo, H.B.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21977127 and 21877134

Revision History  

• Version 1.0: 2022-04-13
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description