7SVP

Structure of compound 34 bound to human Phospholipase D2 catalytic domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.290 
  • R-Value Observed: 0.292 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of Phospholipase D Inhibitors with Improved Drug-like Properties and Central Nervous System Penetrance.

May-Dracka, T.L.Gao, F.Hopkins, B.T.Hronowski, X.Chen, T.Chodaparambil, J.V.Metrick, C.M.Cullivan, M.Enyedy, I.Kaliszczak, M.Kankel, M.W.Marx, I.Michell-Robinson, M.A.Murugan, P.Kumar, P.R.Rooney, M.Schuman, E.Sen, A.Wang, T.Ye, T.Peterson, E.A.

(2022) ACS Med Chem Lett 13: 665-673

  • DOI: https://doi.org/10.1021/acsmedchemlett.1c00682
  • Primary Citation of Related Structures:  
    7SVP

  • PubMed Abstract: 

    Phospholipase D (PLD) is a phospholipase enzyme responsible for hydrolyzing phosphatidylcholine into the lipid signaling molecule, phosphatidic acid, and choline. From a therapeutic perspective, PLD has been implicated in human cancer progression as well as a target for neurodegenerative diseases, including Alzheimer's. Moreover, knockdown of PLD rescues the ALS phenotype in multiple Drosophila models of ALS (amyotrophic lateral sclerosis) and displays modest motor benefits in an SOD1 ALS mouse model. To further validate whether inhibiting PLD is beneficial for the treatment of ALS, a brain penetrant small molecule inhibitor with suitable PK properties to test in an ALS animal model is needed. Using a combination of ligand-based drug discovery and structure-based design, a dual PLD1/PLD2 inhibitor was discovered that is single digit nanomolar in the Calu-1 cell assay and has suitable PK properties for in vivo studies. To capture the in vivo measurement of PLD inhibition, a transphosphatidylation pharmacodynamic LC-MS assay was developed, in which a dual PLD1/PLD2 inhibitor was found to reduce PLD activity by 15-20-fold.


  • Organizational Affiliation

    Biotherapeutic and Medicinal Sciences, Neuromuscular & Movement Disorders Research Unit, Research and Early Development Biomarkers, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phospholipase D2A [auth C],
B [auth A],
C [auth B],
D
640Homo sapiensMutation(s): 0 
Gene Names: PLD2
EC: 3.1.4.4
UniProt & NIH Common Fund Data Resources
Find proteins for O14939 (Homo sapiens)
Explore O14939 
Go to UniProtKB:  O14939
PHAROS:  O14939
GTEx:  ENSG00000129219 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14939
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.290 
  • R-Value Observed: 0.292 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.721α = 90
b = 132.238β = 100.649
c = 113.861γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2023-08-23
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-25
    Changes: Refinement description