5JAU

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: 1.95 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.202 

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
  • Primary Citation of Related Structures:  

  • 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

    Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Platelet-activating factor acetylhydrolase
A
388Homo sapiensMutation(s): 0 
Gene Names: PLA2G7 (PAFAH)
EC: 3.1.1.47
Find proteins for Q13093 (Homo sapiens)
Go to Gene View: PLA2G7
Go to UniProtKB:  Q13093
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6HU
Query on 6HU

Download SDF File 
Download CCD File 
A
(2S)-3-(3-{[4-(2-aminoethoxy)-2',6-dimethyl[1,1'-biphenyl]-3-yl]amino}-1H-pyrazol-1-yl)-2-methoxypropan-1-ol
C23 H30 N4 O3
PUPHJJGGIHFEJD-SFHVURJKSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6HUIC50: 1.4 - 18 nM (100) BINDINGDB
6HUIC50: 1.4 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 99.783α = 90.00
b = 90.533β = 111.83
c = 51.499γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
d*TREKdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Database references
  • Version 1.2: 2019-10-16
    Type: Data collection