9G76 | pdb_00009g76

Crystal structure of ASGPR with bound GalNAc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.233 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Trivalent siRNA-Conjugates with Guanosine as ASGPR-Binder Show Potent Knock-Down In Vivo.

Hofmeister, A.Jahn-Hofmann, K.Brunner, B.Helms, M.Metz-Weidmann, C.Poeverlein, C.Zech, G.Li, Z.Hessler, G.Schreuder, H.Elshorst, B.Krack, A.Kurz, M.Heubel, C.Scheidler, S.

(2025) J Med Chem 68: 6193-6209

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02275
  • Primary Citation of Related Structures:  
    9G76, 9G7D, 9G7E

  • PubMed Abstract: 

    To increase the chemical space around the well-known GalNAc-ligand as ASGPR-binder, a high-throughput screening campaign was performed, testing approximately 550,000 compounds. After evaluation of the potential screening hits, only one compound, which showed high similarity with guanosine nucleosides, was chosen for further profiling. Crystal structure analysis revealed the coordination of the Ca 2+ -ion within the ASGPR-binding site by the cis -diol motif of the ribose unit as well as an additional π-π-interaction of the purine heterocycle to tryptophan-243. Based on these findings, guanosine was attached via the 5'-OH group to a recently described morpholino-based nucleotide using two different linker units. The resulting morpholino-guanosine building blocks were conjugated to the 5'-end of a literature-known transthyretin targeting small interfering RNA (siRNA), leading to trivalent siRNA-guanosine conjugates, which were tested for their TTR knockdown and exhibited similar potencies as the analogous GalNAc-conjugates in vitro and in vivo.


  • Organizational Affiliation
    • Sanofi R&D, Industrial Park Hoechst, 65926 Frankfurt am Main, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Asialoglycoprotein receptor 1153Homo 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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NGA (Subject of Investigation/LOI)
Query on NGA

Download Ideal Coordinates CCD File 
G [auth A]2-acetamido-2-deoxy-beta-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-JAJWTYFOSA-N
A2G (Subject of Investigation/LOI)
Query on A2G

Download Ideal Coordinates CCD File 
F [auth A]2-acetamido-2-deoxy-alpha-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free:  0.233 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.082α = 90
b = 32.641β = 91.89
c = 40.702γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
XDSdata reduction
autoPROCdata scaling
Aimlessdata scaling
STARANISOdata scaling
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateGermanyN.A.

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Database references