Fragment-based inhibitors of Lipoprotein associated Phospholipase A2

Experimental Data Snapshot

  • Resolution: 2.17 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

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Ligand Structure Quality Assessment 

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Fragment-Based Approach to the Development of an Orally Bioavailable Lactam Inhibitor of Lipoprotein-Associated Phospholipase A2 (Lp-PLA2).

Woolford, A.J.Day, P.J.Beneton, V.Berdini, V.Coyle, J.E.Dudit, Y.Grondin, P.Huet, P.Lee, L.Y.Manas, E.S.McMenamin, R.L.Murray, C.W.Page, L.W.Patel, V.K.Potvain, F.Rich, S.J.Sang, Y.Somers, D.O.Trottet, L.Wan, Z.Zhang, X.

(2016) J Med Chem 59: 10738-10749

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b01427
  • Primary Citation of Related Structures:  
    5LYY, 5LZ2, 5LZ4, 5LZ5, 5LZ7, 5LZ8, 5LZ9

  • PubMed Abstract: 

    Lp-PLA 2 has been explored as a target for a number of inflammation associated diseases, including cardiovascular disease and dementia. This article describes the discovery of a new fragment derived chemotype that interacts with the active site of Lp-PLA 2 . The starting fragment hit was discovered through an X-ray fragment screen and showed no activity in the bioassay (IC 50 > 1 mM). The fragment hit was optimized using a variety of structure-based drug design techniques, including virtual screening, fragment merging, and improvement of shape complementarity. A novel series of Lp-PLA 2 inhibitors was generated with low lipophilicity and a promising pharmacokinetic profile.

  • Organizational Affiliation

    Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Platelet-activating factor acetylhydrolase388Homo sapiensMutation(s): 0 
Gene Names: PLA2G7PAFAH
UniProt & NIH Common Fund Data Resources
Find proteins for Q13093 (Homo sapiens)
Explore Q13093 
Go to UniProtKB:  Q13093
PHAROS:  Q13093
GTEx:  ENSG00000146070 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13093
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 7BJ

Download Ideal Coordinates CCD File 
B [auth A]3-[2-(4-fluoranylphenoxy)ethyl]-1,3-diazaspiro[4.5]decane-2,4-dione
C16 H19 F N2 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
7BJ BindingDB:  5LYY IC50: 1.40e+4 (nM) from 1 assay(s)
Binding MOAD:  5LYY IC50: 1.40e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.17 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.924α = 90
b = 91.157β = 111.88
c = 51.333γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Data collection, Database references