3HC8

Investigation of Aminopyridiopyrazinones as PDE5 Inhibitors: Evaluation of Modifications to the Central Ring System.

• PDB DOI: https://doi.org/10.2210/pdb3HC8/pdb

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


• Deposited: 2009-05-05 Released: 2009-07-07 
• Deposition Author(s): Hughes, R.O., Stallings, W.C., Cubbage, J.W., Williams, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.230 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

Investigation of aminopyridiopyrazinones as PDE5 inhibitors: Evaluation of modifications to the central ring system.

Hughes, R.O., Walker, J.K., Cubbage, J.W., Fobian, Y.M., Rogier, D.J., Heasley, S.E., Blevis-Bal, R.M., Benson, A.G., Owen, D.R., Jacobsen, E.J., Freskos, J.N., Molyneaux, J.M., Brown, D.L., Stallings, W.C., Acker, B.A., Maddux, T.M., Tollefson, M.B., Williams, J.M., Moon, J.B., Mischke, B.V., Rumsey, J.M., Zheng, Y., Macinnes, A., Bond, B.R., Yu, Y.

(2009) Bioorg Med Chem Lett 19: 4092-4096

• PubMed: 19539468 
• DOI: https://doi.org/10.1016/j.bmcl.2009.06.004
• Primary Citation of Related Structures:  
  3HC8


• PubMed Abstract: 
  

  Efforts to improve the potency and physical properties of the aminopyridiopyrazinone class of PDE5 inhibitors through modification of the core ring system are described. Five new ring systems are evaluated and features that impart improved potency and improved solubility are delineated.

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Organizational Affiliation: 

Pfizer Global Research and Development, 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: 37.93 kDa 
• Atom Count: 2,839 
• Modelled Residue Count: 324 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cGMP-specific 3',5'-cyclic phosphodiesterase,cAMP-specific 3',5'-cyclic phosphodiesterase 4A	A	324	Homo sapiens	Mutation(s): 0  Gene Names: PDE5A, PDE5, PDE4A, DPDE2 EC: 3.1.4.35 (PDB Primary Data), 3.1.4.53 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O76074 (Homo sapiens) Explore O76074  Go to UniProtKB:  O76074
PHAROS:  O76074 GTEx:  ENSG00000138735
Find proteins for P27815 (Homo sapiens) Explore P27815  Go to UniProtKB:  P27815
PHAROS:  P27815 GTEx:  ENSG00000065989
UniProt Groups	P27815O76074

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PD4	B [auth A]	6-(6-methoxypyridin-3-yl)-2-[(2-morpholin-4-ylethyl)amino]-4-(2-propoxyethyl)pyrido[2,3-b]pyrazin-3(4H)-one C24 H32 N6 O4 KSAKYDGQTISGJC-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PD4	BindingDB:  3HC8	IC50: min: 2.4, max: 2.9 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.230 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.691	α = 90
b = 77.085	β = 101.93
c = 77.514	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-07 
Deposition Author(s): Hughes, R.O., Stallings, W.C., Cubbage, J.W., Williams, J.M.

Revision History  

• Version 1.0: 2009-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-06-21
  Changes: Advisory, Database references, Source and taxonomy, Structure summary
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2018-01-24
  Changes: Structure summary
• Version 1.5: 2023-07-26
  Changes: Database references, Derived calculations
• Version 1.6: 2024-05-22
  Changes: Data collection