Compound binding to Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA2)discovered through fragment screening

Experimental Data Snapshot

  • Resolution: 2.05 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 

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Exploitation of a Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA2) Discovered through X-ray Fragment Screening.

Woolford, A.J.Pero, J.E.Aravapalli, S.Berdini, V.Coyle, J.E.Day, P.J.Dodson, A.M.Grondin, P.Holding, F.P.Lee, L.Y.Li, P.Manas, E.S.Marino, J.Martin, A.C.McCleland, B.W.McMenamin, R.L.Murray, C.W.Neipp, C.E.Page, L.W.Patel, V.K.Potvain, F.Rich, S.Rivero, R.A.Smith, K.Somers, D.O.Trottet, L.Velagaleti, R.Williams, G.Xie, R.

(2016) J Med Chem 59: 5356-5367

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b00212
  • Primary Citation of Related Structures:  
    5JAD, 5JAH, 5JAL, 5JAN, 5JAO, 5JAP, 5JAR, 5JAS, 5JAT, 5JAU

  • PubMed Abstract: 

    Elevated levels of human lipoprotein-associated phospholipase A2 (Lp-PLA2) are associated with cardiovascular disease and dementia. A fragment screen was conducted against Lp-PLA2 in order to identify novel inhibitors. Multiple fragment hits were observed in different regions of the active site, including some hits that bound in a pocket created by movement of a protein side chain (approximately 13 Å from the catalytic residue Ser273). Using structure guided design, we optimized a fragment that bound in this pocket to generate a novel low nanomolar chemotype, which did not interact with the catalytic residues.

  • 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
Binding Affinity Annotations 
IDSourceBinding Affinity
FB2 Binding MOAD:  5JAD Kd: 3.40e+6 (nM) from 1 assay(s)
BindingDB:  5JAD Kd: 3.40e+6 (nM) from 1 assay(s)
IC50: 1.00e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.05 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.97α = 90
b = 91.029β = 112.05
c = 51.191γ = 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: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-06-22
    Changes: Database references
  • Version 1.2: 2016-12-14
    Changes: Structure summary