5LZ2

Fragment-based inhibitors of Lipoprotein associated Phospholipase A2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.228 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 7BXClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

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.


Macromolecules
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
EC: 3.1.1.47
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.971α = 90
b = 90.649β = 111.82
c = 51.321γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 7BXClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2022-07-13
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.2: 2024-06-19
    Changes: Data collection