5U09

High-resolution crystal structure of the human CB1 cannabinoid receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.180

Literature

Macromolecules
Sequence Display for 5U09

Classification: MEMBRANE PROTEIN

Total Structure Weight: 59250.68

Macromolecule Entities
Molecule Chains Length Organism Details
Cannabinoid receptor 1,GlgA glycogen synthase A 508 Homo sapiens Pyrococcus abyssi Fragment: P21554 residues 90-301, 333-421 and Q9V2J8 residues 218-413
Mutation: T210A
Gene Name(s): CNR1 Gene View CNR PAB2292
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: G Protein-Coupled Receptors (GPCRs)

Protein Name: CB1 cannabinoid receptor complexed with stabilizing antagonist AM6538


Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
7DY
Query on 7DY

A N-[(2S,3S)-4-(4-chlorophenyl)-3-(3-cyanophenyl)butan- 2-yl]-2-methyl-2-{[5-(trifluoromethyl)pyridin- 2-yl]oxy}propanamide
C27 H25 Cl F3 N3 O2
QLYKJCMUNUWAGO-GAJHUEQPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

A DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
7DY EC50: 2.4 nM (93) BindingDB
IC50: 0.29 - 0.86 nM (93) BindingDB
Ki: 0.3 nM (93) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.180
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 50.65 α = 90.00
b = 80.38 β = 91.72
c = 81.18 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-11-23
  • Released Date: 2016-12-07
  • Deposition author(s): Shao, Z.H., Yin, J., Rosenbaum, D.
  • This entry supercedes: 5TJV

Revision History

  • Version 1_0: 2016-12-07

    Type: Initial release