5I8P | pdb_00005i8p

Crystal structure of LP_PLA2 in complex with novel inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5I8P/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-02-19 Released: 2016-06-15 
• Deposition Author(s): Liu, Q.F., Xu, Y.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 
  0.275 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

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

• PubMed: 27078579 
• DOI: https://doi.org/10.1021/acs.jmedchem.6b00282
• Primary Citation Related Structures: 
  5I8P, 5I9I


• 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 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.

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Organizational Affiliation: 
• School of Life Science and Technology, ShanghaiTech University , Shanghai 200031, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 88.97 kDa 
• Atom Count: 5,736 
• Modeled Residue Count: 735 
• Deposited Residue Count: 776 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Platelet-activating factor acetylhydrolase	A, B	388	Homo sapiens	Mutation(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 GTEx:  ENSG00000146070

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VQ7	C [auth A], D [auth B]	6-[1,1-bis(oxidanylidene)-1,4-thiazinan-4-yl]-4-[[4-[4-chloranyl-3-(trifluoromethyl)phenoxy]-3,5-bis(fluoranyl)phenyl]methoxy]-1-methyl-pyrimidin-2-one C23 H19 Cl F5 N3 O5 S FLCSHCSBIFPQJJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
VQ7	BindingDB:  5I8P	Kd: 185 (nM) from 1 assay(s)
		IC50: 1.7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.275 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.82	α = 90
b = 82.75	β = 115.44
c = 96.39	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• 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
  
• Version 1.1: 2017-10-04
  Changes: Data collection, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description