9G6W | pdb_00009g6w

L-SIGN CRD in complex with Man96.

PDB DOI: https://doi.org/10.2210/pdb9G6W/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-07-19 Released: 2025-07-30
Deposition Author(s): Thepaut, M., Cavazzoli, G., Bernardi, A., Fieschi, F.
Funding Organization(s): Grenoble Alliance for Integrated Structural Cell Biology (GRAL), Ministero dell Universita e della Ricerca

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.290 (Depositor), 0.320 (DCC)
R-Value Work:
0.228 (Depositor), 0.264 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Increasing the Chemical Space of L-SIGN Specific Glycomimetics.

Cavazzoli, G., Delaunay, C., Pollastri, S., Panzeri, A., Sattin, S., Thepaut, M., Belvisi, L., Fieschi, F., Bernardi, A.

(2025) J Med Chem 68: 22530-22546

PubMed: 41108276 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.jmedchem.5c01448
Primary Citation Related Structures:
9G6W

PubMed Abstract:
Selective ligands for the C-type lectin receptor L-SIGN offer promising avenues in antiviral therapies and for tissue-specific delivery. We recently reported that a guanidine-bearing modified mannose glycomimetic, called Man84 , binds to L-SIGN with micromolar affinity and high-selectivity against the homologue lectin DC-SIGN. Here we describe a series of Man84 isosteres (ligands 2-11 ) that maintain or improve on this selectivity. The affinity of the ligands for L-SIGN, as well as their selectivity against DC-SIGN, were evaluated by Surface Plasmon Resonance inhibition assays using immobilized SARS-CoV-2 Spike protein. Compounds 4 , 5 and 9 were found to bind to L-SIGN with low micromolar affinity and 50-94-fold selectivity, thus matching or exceeding the performance of Man84 . The crystal structure of the L-SIGN CRD/ 4 complex was solved and highlighted the critical role of a bidentate H-bond interaction of the ligands with the side chain of E370 in L-SIGN.

Organizational Affiliation

Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, Milano 20133, Italy.

Macromolecule Content

Total Structure Weight: 32.83 kDa
Atom Count: 2,304
Modeled Residue Count: 256
Deposited Residue Count: 274
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 1 of C-type lectin domain family 4 member M	A, B	137	Homo sapiens	Mutation(s): 0 Gene Names: CLEC4M, CD209L, CD209L1, CD299
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H2X3 (Homo sapiens) Explore Q9H2X3 Go to UniProtKB: Q9H2X3
PHAROS: Q9H2X3 GTEx: ENSG00000104938
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H2X3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IIW (Subject of Investigation/LOI) Query on A1IIW Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	C [auth A], I [auth B]	(2~{R},3~{S},4~{R},5~{S},6~{S})-6-(2-chloroethyloxy)-2-(hydroxymethyl)-5-[4-[(imidazolidin-2-ylideneamino)methyl]-1,2,3-triazol-1-yl]oxane-3,4-diol C₁₄ H₂₃ Cl N₆ O₅ SUTPIBBHKSRFDY-MLGHIDQZSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] J [auth B] K [auth B] D [auth A], E [auth A], F [auth A], J [auth B], K [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.290 (Depositor), 0.320 (DCC)
R-Value Work: 0.228 (Depositor), 0.264 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.72	α = 90
b = 105.72	β = 90
c = 59.11	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)	France	CBH-EUR-GS (ANR-17- EURE0003)
Ministero dell Universita e della Ricerca	Italy	PRIN 20224LLK82