5JQ1

Efficient targeting of the asialoglycoprotein receptor by polyvalent display of a compact galactosamine mimic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Efficient Liver Targeting by Polyvalent Display of a Compact Ligand for the Asialoglycoprotein Receptor.

Sanhueza, C.A.Baksh, M.M.Thuma, B.Roy, M.D.Dutta, S.Preville, C.Chrunyk, B.A.Beaumont, K.Dullea, R.Ammirati, M.Liu, S.Gebhard, D.Finley, J.E.Salatto, C.T.King-Ahmad, A.Stock, I.Atkinson, K.Reidich, B.Lin, W.Kumar, R.Tu, M.Menhaji-Klotz, E.Price, D.A.Liras, S.Finn, M.G.Mascitti, V.

(2017) J Am Chem Soc 139: 3528-3536

  • DOI: https://doi.org/10.1021/jacs.6b12964
  • Primary Citation of Related Structures:  
    5JPV, 5JQ1

  • PubMed Abstract: 

    A compact and stable bicyclic bridged ketal was developed as a ligand for the asialoglycoprotein receptor (ASGPR). This compound showed excellent ligand efficiency, and the molecular details of binding were revealed by the first X-ray crystal structures of ligand-bound ASGPR. This analogue was used to make potent di- and trivalent binders of ASGPR. Extensive characterization of the function of these compounds showed rapid ASGPR-dependent cellular uptake in vitro and high levels of liver/plasma selectivity in vivo. Assessment of the biodistribution in rodents of a prototypical Alexa647-labeled trivalent conjugate showed selective hepatocyte targeting with no detectable distribution in nonparenchymal cells. This molecule also exhibited increased ASGPR-directed hepatocellular uptake and prolonged retention compared to a similar GalNAc derived trimer conjugate. Selective release in the liver of a passively permeable small-molecule cargo was achieved by retro-Diels-Alder cleavage of an oxanorbornadiene linkage, presumably upon encountering intracellular thiol. Therefore, the multicomponent construct described here represents a highly efficient delivery vehicle to hepatocytes.


  • Organizational Affiliation

    School of Chemistry & Biochemistry, Georgia Institute of Technology , 901 Atlantic Avenue, Atlanta, Georgia 30332, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Asialoglycoprotein receptor 1
A, B
145Homo sapiensMutation(s): 0 
Gene Names: ASGR1CLEC4H1
UniProt & NIH Common Fund Data Resources
Find proteins for P07306 (Homo sapiens)
Explore P07306 
Go to UniProtKB:  P07306
PHAROS:  P07306
GTEx:  ENSG00000141505 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07306
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZPF
Query on ZPF

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
N-[(1S,2R,3R,4R,5S)-2,3-dihydroxy-1-(hydroxymethyl)-6,8-dioxabicyclo[3.2.1]octan-4-yl]acetamide
C9 H15 N O6
HXIYAFJXGOVJDG-HXLXBVJFSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
H [auth B]
I [auth B]
C [auth A],
D [auth A],
E [auth A],
H [auth B],
I [auth B],
K [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
ZPF BindingDB:  5JQ1 Kd: 7180 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.08α = 90
b = 59.49β = 93.18
c = 68.65γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2017-06-14 
  • Deposition Author(s): Liu, S.

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description