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 

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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: 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) ...

    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 acetylhydrolase388Homo sapiensMutation(s): 0 
Gene Names: PLA2G7, PAFAH
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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6HW
Query on 6HW
Download Ideal Coordinates CCD File 
E [auth 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 Ideal Coordinates CCD File 
D [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
6HW Binding MOAD:  5JAS IC50: 1700 (nM) from 1 assay(s)
BindingDB:  5JAS IC50: 1700 (nM) from 1 assay(s)
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

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Ligand Structure Quality Assessment 


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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