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

Literature

Macromolecules
Sequence Display for 5I9I

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 89337.30

Macromolecule Entities
Molecule Chains Length Organism Details
Platelet-activating factor acetylhydrolase A, B 388 Homo sapiens EC#: 3.1.1.47 IUBMB
Fragment: UNP residues 47-429
Gene Name(s): PLA2G7 Gene View PAFAH
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
5HV
Query on 5HV

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 (Synonym)
C36 H38 F4 N4 O2 S
WDPFJWLDPVQCAJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

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 = 115.90 α = 90.00
b = 82.41 β = 115.50
c = 96.47 γ = 90.00

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