8WKF | pdb_00008wkf

Rational Design of Highly Selective PDE5 inhibitors for the Treatment of Idiopathic Pulmonary Fibrosis

• PDB DOI: https://doi.org/10.2210/pdb8WKF/pdb

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


• Deposited: 2023-09-27 Released: 2024-10-02 
• Deposition Author(s): Zhang, F.C., Huang, Y.Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.248 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.196 (DCC) 

Starting Model: experimental

Literature

Rational Design of Highly Selective PDE5 inhibitors for the Treatment of Idiopathic Pulmonary Fibrosis

Zhang, F.C., Huang, Y.Y.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 39.03 kDa 
• Atom Count: 2,492 
• Modeled Residue Count: 292 
• Deposited Residue Count: 333 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cGMP-specific 3',5'-cyclic phosphodiesterase	A	333	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
WD3 (Subject of Investigation/LOI)	B [auth A]	3-[2-[[5-chloranyl-2-[(3-fluorophenyl)methylamino]phenyl]methyl]-4-oxidanylidene-3~{H}-quinazolin-7-yl]prop-2-enoic acid C25 H19 Cl F N3 O3 GAOVVHYYICHQJM-WEVVVXLNSA-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: 2.40 Å
• R-Value Free:  0.248 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.196 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.428	α = 90
b = 74.428	β = 90
c = 131.478	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-02 
Deposition Author(s): Zhang, F.C., Huang, 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: 2024-10-02
  Type: Initial release