5LZ5

Fragment-based inhibitors of Lipoprotein associated Phospholipase A2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7K4
Query on 7K4

Download Ideal Coordinates CCD File 
D [auth A]2-fluoranyl-5-[2-[(4~{S})-4-methyl-2-oxidanylidene-4-phenyl-pyrrolidin-1-yl]ethoxy]benzenecarbonitrile
C20 H19 F N2 O2
WMVNTKWNIVSPIC-HXUWFJFHSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
7K4 Binding MOAD:  5LZ5 Kd: 450 (nM) from 1 assay(s)
BindingDB:  5LZ5 IC50: 1600 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.091α = 90
b = 91.494β = 111.92
c = 48.648γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-21
    Type: Initial release