5JAH

Exploitation of a Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA<sub>2</sub>) Discovered Through X-Ray Fragment Screening


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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

    Centre de Recherches Francois Hyafil, GlaxoSmithKline , 25-27 Avenue du Québec, Les Ulis, France.


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
GTEx:  ENSG00000146070 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13093
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6HQ
Query on 6HQ

Download Ideal Coordinates CCD File 
C [auth A]1,5,5-trimethylimidazolidine-2,4-dione
C6 H10 N2 O2
ZNYIPTYJBRGSSL-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.03α = 90
b = 91.309β = 112
c = 51.316γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
d*TREKdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2016-05-25 
  • Deposition Author(s): Day, P.J.

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: 2019-10-16
    Changes: Data collection