3TGE

A novel series of potent and selective PDE5 inhibitor1

• PDB DOI: https://doi.org/10.2210/pdb3TGE/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2011-08-17 Released: 2011-11-09 
• Deposition Author(s): Han, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.194 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 

Literature

Investigation of the pyrazinones as PDE5 inhibitors: Evaluation of regioisomeric projections into the solvent region.

Hughes, R.O., Maddux, T., Joseph Rogier, D., Lu, S., Walker, J.K., Jon Jacobsen, E., Rumsey, J.M., Zheng, Y., Macinnes, A., Bond, B.R., Han, S.

(2011) Bioorg Med Chem Lett 21: 6348-6352

• PubMed: 21955943 
• DOI: https://doi.org/10.1016/j.bmcl.2011.08.106
• Primary Citation of Related Structures:  
  3TGE, 3TGG


• PubMed Abstract: 
  

  We describe the design, synthesis and profiling of a novel series of PDE5 inhibitors. We take advantage of an alternate projection into the solvent region to identify compounds with excellent potency, selectivity and pharmacokinetic profiles.

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Organizational Affiliation: 

Pfizer Global Research and Development, 700 Chesterfield Parkway West, St. Louis, MO 63017, USA. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 38.17 kDa 
• Atom Count: 2,808 
• Modelled Residue Count: 324 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cGMP-specific 3',5'-cyclic phosphodiesterase	A	326	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
TGE	D [auth A]	7-(6-methoxypyridin-3-yl)-3-{[2-(morpholin-4-yl)ethyl]amino}-1-(2-propoxyethyl)pyrido[3,4-b]pyrazin-2(1H)-one C24 H32 N6 O4 OFRWMWHKNKWEHT-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TGE	PDBBind:  3TGE	IC50: 0.07 (nM) from 1 assay(s)
	BindingDB:  3TGE	IC50: 0.07 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.194 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.63	α = 90
b = 77.311	β = 101.19
c = 78.265	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-09 
Deposition Author(s): Han, S.

Revision History  

• Version 1.0: 2011-11-09
  Type: Initial release
  
• Version 1.1: 2017-08-16
  Changes: Refinement description, Source and taxonomy
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations