5JAP

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: 2.46 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    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) ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Platelet-activating factor acetylhydrolaseA388Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13093
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6HZ
Query on 6HZ

Download Ideal Coordinates CCD File 
E [auth A](2,5-dihydro-1H-pyrrol-1-yl)(2',6-dimethyl[1,1'-biphenyl]-3-yl)methanone
C19 H19 N O
NIOIWNZLGVRPNS-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
D [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
6HZ BindingDB:  5JAP IC50: 230 (nM) from 1 assay(s)
Binding MOAD:  5JAP IC50: 230 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.927α = 90
b = 90.661β = 111.55
c = 51.303γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
d*TREKdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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