4Z36

Crystal Structure of Human Lysophosphatidic Acid Receptor 1 in complex with ONO-3080573


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.272 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of Antagonist Bound Human Lysophosphatidic Acid Receptor 1.

Chrencik, J.E.Roth, C.B.Terakado, M.Kurata, H.Omi, R.Kihara, Y.Warshaviak, D.Nakade, S.Asmar-Rovira, G.Mileni, M.Mizuno, H.Griffith, M.T.Rodgers, C.Han, G.W.Velasquez, J.Chun, J.Stevens, R.C.Hanson, M.A.

(2015) Cell 161: 1633-1643

  • DOI: 10.1016/j.cell.2015.06.002
  • Primary Citation of Related Structures:  4Z34, 4Z35

  • PubMed Abstract: 
  • Lipid biology continues to emerge as an area of significant therapeutic interest, particularly as the result of an enhanced understanding of the wealth of signaling molecules with diverse physiological properties. This growth in knowledge is epitomiz ...

    Lipid biology continues to emerge as an area of significant therapeutic interest, particularly as the result of an enhanced understanding of the wealth of signaling molecules with diverse physiological properties. This growth in knowledge is epitomized by lysophosphatidic acid (LPA), which functions through interactions with at least six cognate G protein-coupled receptors. Herein, we present three crystal structures of LPA1 in complex with antagonist tool compounds selected and designed through structural and stability analyses. Structural analysis combined with molecular dynamics identified a basis for ligand access to the LPA1 binding pocket from the extracellular space contrasting with the proposed access for the sphingosine 1-phosphate receptor. Characteristics of the LPA1 binding pocket raise the possibility of promiscuous ligand recognition of phosphorylated endocannabinoids. Cell-based assays confirmed this hypothesis, linking the distinct receptor systems through metabolically related ligands with potential functional and therapeutic implications for treatment of disease.


    Organizational Affiliation

    Department of Structural Discovery, Receptos, San Diego, CA 92121, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysophosphatidic acid receptor 1,Soluble cytochrome b562
A
459Escherichia coliHomo sapiens
This entity is chimeric
Gene Names: cybC, LPAR1 (EDG2, LPA1)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
LPA1 Lysophosphatidic Acid Receptor 1 in complex with ONO-9780307
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Find proteins for Q92633 (Homo sapiens)
Go to Gene View: LPAR1
Go to UniProtKB:  Q92633
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ON3
Query on ON3

Download SDF File 
Download CCD File 
A
1-(4-{[(2S,3R)-2-(2,3-dihydro-1H-inden-2-yloxy)-3-(3,5-dimethoxy-4-methylphenyl)-3-hydroxypropyl]oxy}phenyl)cyclopropanecarboxylic acid
ONO-3080573
C31 H34 O7
FVESDCZDESZGHA-URLMMPGGSA-N
 Ligand Interaction
1WV
Query on 1WV

Download SDF File 
Download CCD File 
A
(2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate
C17 H32 O4
LVBAGTJIDOCNIJ-INIZCTEOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.272 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 34.350α = 90.00
b = 111.930β = 90.00
c = 153.960γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
BUSTERrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-07-01
    Type: Database references