5JPV | pdb_00005jpv

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.225 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5JPV

This is version 2.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 34.98 kDa 
  • Atom Count: 2,471 
  • Modeled Residue Count: 256 
  • Deposited Residue Count: 290 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose
C, D
2N/A
Glycosylation Resources
GlyTouCan: G88362QR
GlyCosmos: G88362QR
GlyGen: G88362QR

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
GAL BindingDB:  5JPV Kd: 1.46e+6 (nM) from 1 assay(s)
IC50: 1.05e+6 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.225 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.1α = 90
b = 59.785β = 93.27
c = 68.818γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-09-27
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-20
    Changes: Structure summary