8BPY

X-RAY STRUCTURE OF PDE9A IN COMPLEX WITH Inhibitor 13A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.250 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

BAY-7081: A Potent, Selective, and Orally Bioavailable Cyanopyridone-Based PDE9A Inhibitor.

Meibom, D.Micus, S.Andreevski, A.L.Anlauf, S.Bogner, P.von Buehler, C.J.Dieskau, A.P.Dreher, J.Eitner, F.Fliegner, D.Follmann, M.Gericke, K.M.Maassen, S.Meyer, J.Schlemmer, K.H.Steuber, H.Tersteegen, A.Wunder, F.

(2022) J Med Chem 65: 16420-16431

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01267
  • Primary Citation of Related Structures:  
    8BPY

  • PubMed Abstract: 

    Despite advances in the treatment of heart failure in recent years, options for patients are still limited and the disease is associated with considerable morbidity and mortality. Modulating cyclic guanosine monophosphate levels within the natriuretic peptide signaling pathway by inhibiting PDE9A has been associated with beneficial effects in preclinical heart failure models. We herein report the identification of BAY-7081, a potent, selective, and orally bioavailable PDE9A inhibitor with very good aqueous solubility starting from a high-throughput screening hit. Key aspect of the optimization was a switch in metabolism of our lead structures from glucuronidation to oxidation. The switch proved being essential for the identification of compounds with improved pharmacokinetic profiles. By studying a tool compound in a transverse aortic constriction mouse model, we were able to substantiate the relevance of PDE9A inhibition in heart diseases.


  • Organizational Affiliation

    Bayer AG, 42113 Wuppertal, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
A, B
315Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76083
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R4I (Subject of Investigation/LOI)
Query on R4I

Download Ideal Coordinates CCD File 
F [auth A](8~{S})-6-[2-(2,3-dihydroindol-1-yl)-2-oxidanylidene-ethyl]-4-(4-methylphenyl)-2-oxidanylidene-8-propyl-1,5,7,8-tetrahydro-1,6-naphthyridine-3-carbonitrile
C29 H30 N4 O2
TVUOEVCKUGISBU-QFIPXVFZSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.250 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 222.423α = 90
b = 222.423β = 90
c = 120.257γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2022-12-28 
  • Deposition Author(s): Steuber, H.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-28
    Type: Initial release
  • Version 1.1: 2023-01-04
    Changes: Database references
  • Version 2.0: 2023-01-11
    Changes: Advisory, Data collection, Derived calculations, Non-polymer description, Structure summary