6LZZ | pdb_00006lzz

Crystal structure of the PDE9 catalytic domain in complex with inhibitor 4a

• PDB DOI: https://doi.org/10.2210/pdb6LZZ/pdb

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


• Deposited: 2020-02-19 Released: 2021-02-24 
• Deposition Author(s): Huang, Y.Y., Wu, Y., Luo, H.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.295 (Depositor), 0.296 (DCC) 
• R-Value Work: 
  0.253 (Depositor), 0.254 (DCC) 
• R-Value Observed: 
  0.255 (Depositor) 

Starting Model: experimental

Literature

Identification of phosphodiesterase-9 as a novel target for pulmonary arterial hypertension by using highly selective and orally bioavailable inhibitors

Tian, Y.J., Zhou, Q., Zhang, P., Jiang, M.Y., Zhang, B., Wu, X.N., Zhang, C., Li, Z., Wu, Y., Chen, Z., Luo, H.B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 77.1 kDa 
• Atom Count: 5,504 
• Modeled Residue Count: 638 
• Deposited Residue Count: 644 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	A, B	322	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
EZU (Subject of Investigation/LOI)	E [auth A], H [auth B]	1-cyclopentyl-6-[[(2R)-1-(2-oxa-6-azaspiro[3.3]heptan-6-yl)-1-oxidanylidene-propan-2-yl]amino]-5H-pyrazolo[3,4-d]pyrimidin-4-one C18 H24 N6 O3 KCKFQVCSNMDMEM-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: 2.40 Å
• R-Value Free:  0.295 (Depositor), 0.296 (DCC) 
• R-Value Work:  0.253 (Depositor), 0.254 (DCC) 
• R-Value Observed: 0.255 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.383	α = 90
b = 103.383	β = 90
c = 268.366	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-24 
Deposition Author(s): Huang, Y.Y., Wu, Y., Luo, H.B.

Revision History  

• Version 1.0: 2021-02-24
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary