1H9U

THE STRUCTURE OF THE HUMAN RETINOID-X-RECEPTOR BETA LIGAND BINDING DOMAIN IN COMPLEX WITH THE SPECIFIC SYNTHETIC AGONIST LG100268

Structural Biology Knowledgebase: 1H9U SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.306
  • R-Value Work: 0.273

Literature

Macromolecules
Sequence Display for 1H9U

Classification: NUCLEAR RECEPTOR

Total Structure Weight: 101130.98

Macromolecule Entities
Molecule Chains Length Organism Details
RETINOID X RECEPTOR, BETA A, B, C, D 224 Homo sapiens Fragment: LIGAND BINDING DOMAIN RESIDUES 299-522
Gene Name(s): RXRB Gene View NR2B2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
LG2
Query on LG2

A, B, C, D 6-[1-(3,5,5,8,8-PENTAMETHYL-5,6,7,8-TETRAHYDRONAPHTHALEN- 2-YL)CYCLOPROPYL]PYRIDINE-3-CARBOXYLIC ACID
C24 H29 N O2
SLXTWXQUEZSSTJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

A, B, C, D NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
LG2 EC50: 3 - 40 nM (88 - 98) BindingDB
IC50: 8 nM (88) BindingDB
Kd: 3 nM (88) BindingDB
Ki: 3 - 3515 nM (88 - 100) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.306
  • R-Value Work: 0.273
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 123.89 α = 90.00
b = 106.88 β = 122.56
c = 100.59 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-03-21
  • Released Date: 2002-04-03
  • Deposition author(s): Schwabe, J.W.R., Love, J.D., Gooch, J.T.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4