5JAS

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: 0.155 
  • R-Value Observed: 0.159 

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: 10.1021/acs.jmedchem.6b00212
  • Structures With Same Primary Citation

  • 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 obs ...

    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

    GlaxoSmithKline , 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Platelet-activating factor acetylhydrolase
A
388Homo sapiensMutation(s): 0 
Gene Names: PLA2G7PAFAH
EC: 3.1.1.47
Find proteins for Q13093 (Homo sapiens)
Go to UniProtKB:  Q13093
NIH Common Fund Data Resources
PHAROS  Q13093
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6HW
Query on 6HW

Download CCD File 
A
N-(2',6-dimethyl[1,1'-biphenyl]-3-yl)-1,3-thiazol-2-amine
C17 H16 N2 S
OZBQQKIXAODXQL-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6HWIC50:  1700   nM  Binding MOAD
6HWIC50:  1700   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.159 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.496α = 90
b = 90.69β = 111.67
c = 51.253γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
d*TREKdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2016-04-12 
  • Released Date: 2016-05-25 
  • Deposition Author(s): Day, P.J.

Revision History 

  • 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