5I9I

Crystal structure of LP_PLA2 in complex with Darapladib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural and Thermodynamic Characterization of Protein-Ligand Interactions Formed between Lipoprotein-Associated Phospholipase A2 and Inhibitors

Liu, Q.F.Chen, X.D.Chen, W.Y.Yuan, X.J.Su, H.X.Shen, J.H.Xu, Y.C.

(2016) J.Med.Chem. 59: 5115-5120

  • DOI: 10.1021/acs.jmedchem.6b00282
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lipoprotein-associated phospholipase A2 (Lp-PLA2) represents a promising therapeutic target for atherosclerosis and Alzheimer's disease. Here we reported the first crystal structures of Lp-PLA2 bound with reversible inhibitors and the thermodynamic c ...

    Lipoprotein-associated phospholipase A2 (Lp-PLA2) represents a promising therapeutic target for atherosclerosis and Alzheimer's disease. Here we reported the first crystal structures of Lp-PLA2 bound with reversible inhibitors and the thermodynamic characterization of complexes. High rigidity of Lp-PLA2 structure and similar binding modes of inhibitors with completely different scaffolds are revealed. It not only provides the molecular basis for inhibitory activity but also sheds light on the essential features of Lp-PLA2 recognition with reversible inhibitors.


    Organizational Affiliation

    School of Life Science and Technology, ShanghaiTech University , Shanghai 200031, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Platelet-activating factor acetylhydrolase
A, B
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5HV
Query on 5HV

Download SDF File 
Download CCD File 
A, B
N-[2-(diethylamino)ethyl]-2-{2-[(4-fluorobenzyl)sulfanyl]-4-oxo-4,5,6,7-tetrahydro-1H-cyclopenta[d]pyrimidin-1-yl}-N-{[4'-(trifluoromethyl)biphenyl-4-yl]methyl}acetamide
Darapladib
C36 H38 F4 N4 O2 S
WDPFJWLDPVQCAJ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5HVIC50: 0 - 49 nM (100) BINDINGDB
5HVKd: 5 nM (100) BINDINGDB
5HVKi: 110 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 115.900α = 90.00
b = 82.410β = 115.50
c = 96.470γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERmodel building
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-02-20 
  • Released Date: 2016-06-15 
  • Deposition Author(s): Liu, Q.F., Xu, Y.C.

Revision History 

  • Version 1.0: 2016-06-15
    Type: Initial release