2XR6 image
Deposition Date 2010-09-10
Release Date 2011-10-19
Last Version Date 2024-11-13
Entry Detail
PDB ID:
2XR6
Title:
Crystal structure of the complex of the carbohydrate recognition domain of human DC-SIGN with pseudo trimannoside mimic.
Biological Source:
Source Organism:
HOMO SAPIENS (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.35 Å
R-Value Free:
0.16
R-Value Work:
0.14
R-Value Observed:
0.14
Space Group:
P 43 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:CD209 ANTIGEN
Gene (Uniprot):CD209
Mutations:YES
Chain IDs:A
Chain Length:170
Number of Molecules:1
Biological Source:HOMO SAPIENS
Primary Citation
Unique Dc-Sign Clustering Activity of a Small Glycomimetic: A Lesson for Ligand Design.
Acs Chem.Biol. 9 1377 ? (2014)
PMID: 24749535 DOI: 10.1021/CB500054H

Abstact

DC-SIGN is a dendritic cell-specific C-type lectin receptor that recognizes highly glycosylated ligands expressed on the surface of various pathogens. This receptor plays an important role in the early stages of many viral infections, including HIV, which makes it an interesting therapeutic target. Glycomimetic compounds are good drug candidates for DC-SIGN inhibition due to their high solubility, resistance to glycosidases, and nontoxicity. We studied the structural properties of the interaction of the tetrameric DC-SIGN extracellular domain (ECD), with two glycomimetic antagonists, a pseudomannobioside (1) and a linear pseudomannotrioside (2). Though the inhibitory potency of 2, as measured by SPR competition experiments, was 1 order of magnitude higher than that of 1, crystal structures of the complexes within the DC-SIGN carbohydrate recognition domain showed the same binding mode for both compounds. Moreover, when conjugated to multivalent scaffolds, the inhibitory potencies of these compounds became uniform. Combining isothermal titration microcalorimetry, analytical ultracentrifugation, and dynamic light scattering techniques to study DC-SIGN ECD interaction with these glycomimetics revealed that 2 is able, without any multivalent presentation, to cluster DC-SIGN tetramers leading to an artificially overestimated inhibitory potency. The use of multivalent scaffolds presenting 1 or 2 in HIV trans-infection inhibition assay confirms the loss of potency of 2 upon conjugation and the equal efficacy of chemically simpler compound 1. This study documents a unique case where, among two active compounds chemically derived, the compound with the lower apparent activity is the optimal lead for further drug development.

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Primary Citation of related structures