6E6M

Crystal structure of human cellular retinol-binding protein 1 in complex with cannabidiorcin (CBDO)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Abnormal Cannabidiol Modulates Vitamin A Metabolism by Acting as a Competitive Inhibitor of CRBP1.

Silvaroli, J.A.Widjaja-Adhi, M.A.K.Trischman, T.Chelstowska, S.Horwitz, S.Banerjee, S.Kiser, P.D.Blaner, W.S.Golczak, M.

(2019) ACS Chem Biol 14: 434-448

  • DOI: 10.1021/acschembio.8b01070
  • Primary Citation of Related Structures:  
    6E5W, 6E5T, 6E5L, 6E6K, 6E6M

  • PubMed Abstract: 
  • Cellular retinol-binding proteins (CRBPs) facilitate the uptake and intracellular transport of vitamin A. They integrate retinoid metabolism, playing an important role in regulating the synthesis of bioactive vitamin A metabolites. Thus, CRBPs constitute potential pharmacological targets to modulate cellular retinoid status that in turn may have applications in the treatment of certain immunological, metabolic, and ocular disorders ...

    Cellular retinol-binding proteins (CRBPs) facilitate the uptake and intracellular transport of vitamin A. They integrate retinoid metabolism, playing an important role in regulating the synthesis of bioactive vitamin A metabolites. Thus, CRBPs constitute potential pharmacological targets to modulate cellular retinoid status that in turn may have applications in the treatment of certain immunological, metabolic, and ocular disorders. Here we identify abnormal cannabidiol (abn-CBD) as a nonretinoid inhibitor of cellular retinol-binding protein 1 (CRBP1). X-ray crystal structures of CRBP1 in complex with abn-CBD and its derivatives revealed a distinctive mode of protein-ligand interaction and provided a molecular basis for the high affinity and selectivity of this compound. We demonstrated that abn-CBD modulates the flux of retinoids via the retinoid cycle in vivo. Furthermore, the biological activity of abn-CBD was evidenced by its ability to protect against light-induced retinal damage in Balb/cJ mice. Altogether, our findings indicate that targeting selected CRBPs with a small-molecule inhibitor can potentially lead to the development of new therapeutic agents to counteract diseases with etiologies involving imbalance in retinoid metabolism or signaling.


    Organizational Affiliation

    Department of Medicine, College of Physicians and Surgeons , Columbia University , New York , NY , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Retinol-binding protein 1A, B, C140Homo sapiensMutation(s): 0 
Gene Names: RBP1CRBP1
UniProt & NIH Common Fund Data Resources
Find proteins for P09455 (Homo sapiens)
Explore P09455 
Go to UniProtKB:  P09455
PHAROS:  P09455
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8CB (Subject of Investigation/LOI)
Query on 8CB

Download Ideal Coordinates CCD File 
D [auth A], E [auth B], F [auth C](1'R,2'R)-4,5'-dimethyl-2'-(prop-1-en-2-yl)-1',2',3',4'-tetrahydro[1,1'-biphenyl]-2,6-diol
C17 H22 O2
GKVOVXWEBSQJPA-UONOGXRCSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
8CB Binding MOAD:  6E6M Ki: 1662 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.21α = 90
b = 93.04β = 90
c = 119.82γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Eye Institute (NIH/NEI)United StatesEY023948

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-13
    Type: Initial release
  • Version 1.1: 2019-03-13
    Changes: Data collection
  • Version 1.2: 2019-08-28
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence