8SYC

Crystal structure of PDE3B in complex with GSK4394835A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery and SAR Study of Boronic Acid-Based Selective PDE3B Inhibitors from a Novel DNA-Encoded Library.

Rowley, A.M.Yao, G.Andrews, L.Bedermann, A.Biddulph, R.Bingham, R.Brady, J.J.Buxton, R.Cecconie, T.Cooper, R.Csakai, A.Gao, E.N.Grenier-Davies, M.C.Lawler, M.Lian, Y.Macina, J.Macphee, C.Marcaurelle, L.Martin, J.McCormick, P.Pindoria, R.Rauch, M.Rocque, W.Shen, Y.Shewchuk, L.M.Squire, M.Stebbeds, W.Tear, W.Wang, X.Ward, P.Xiao, S.

(2024) J Med Chem 67: 2049-2065

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01562
  • Primary Citation of Related Structures:  
    8SYC

  • PubMed Abstract: 

    Human genetic evidence shows that PDE3B is associated with metabolic and dyslipidemia phenotypes. A number of PDE3 family selective inhibitors have been approved by the FDA for various indications; however, given the undesirable proarrhythmic effects in the heart, selectivity for PDE3B inhibition over closely related family members (such as PDE3A; 48% identity) is a critical consideration for development of PDE3B therapeutics. Selectivity for PDE3B over PDE3A may be achieved in a variety of ways, including properties intrinsic to the compound or tissue-selective targeting. The high (>95%) active site homology between PDE3A and B represents a massive obstacle for obtaining selectivity at the active site; however, utilization of libraries with high molecular diversity in high throughput screens may uncover selective chemical matter. Herein, we employed a DNA-encoded library screen to identify PDE3B-selective inhibitors and identified potent and selective boronic acid compounds bound at the active site.


  • Organizational Affiliation

    GSK, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cGMP-inhibited 3',5'-cyclic phosphodiesterase 3BA,
B [auth D]
443Homo sapiensMutation(s): 5 
Gene Names: PDE3B
EC: 3.1.4.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q13370 (Homo sapiens)
Explore Q13370 
Go to UniProtKB:  Q13370
PHAROS:  Q13370
GTEx:  ENSG00000152270 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13370
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.586α = 90
b = 78.586β = 90
c = 166.339γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Database references