8XWW | pdb_00008xww

Crystal structure of the catalytic domain of human PDE5A complexed with 2-(3-chlorobenzyl)-4-oxo-3,4-dihydroquinazoline-7-carboxylic acid

• PDB DOI: https://doi.org/10.2210/pdb8XWW/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-01-16 Released: 2025-01-22 
• Deposition Author(s): Zhang, F.C., Huang, Y.Y., Luo, H.B., Wu, Y.Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.267 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.236 (DCC) 

Starting Model: experimental

Literature

Discovery of Highly Potent and Selective PDE5 Inhibitors for the Treatment of Idiopathic Pulmonary Fibrosis

Zhang, F.C., Huang, Y.Y., Luo, H.B., Wu, Y.Y.

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: 40.67 kDa 
• Atom Count: 2,448 
• Modeled Residue Count: 292 
• Deposited Residue Count: 349 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform PDE5A1 of cGMP-specific 3',5'-cyclic phosphodiesterase	A	349	Homo sapiens	Mutation(s): 0  Gene Names: PDE5A, PDE5 EC: 3.1.4.35
UniProt & NIH Common Fund Data Resources
Find proteins for O76074 (Homo sapiens) Explore O76074  Go to UniProtKB:  O76074
PHAROS:  O76074 GTEx:  ENSG00000138735

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D5K (Subject of Investigation/LOI)	B [auth A]	2-[(3-chlorophenyl)methyl]-4-oxidanylidene-3~{H}-quinazoline-7-carboxylic acid C16 H11 Cl N2 O3 ZKCXRRXBYVUYSJ-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.267 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.236 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.261	α = 90
b = 74.261	β = 90
c = 131.943	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Zhang, F.C., Huang, Y.Y., Luo, H.B., Wu, Y.Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21977127
National Natural Science Foundation of China (NSFC)	China	22077143

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release