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Ligandly | Molecular interaction research

Molecular interaction research

Explore protein–ligand interactions with clarity.

Ligandly brings together research tools, methods, and visualization resources for studying protein–ligand interactions. Explore the science, then open the analysis applications.

Explore available tools ↗View example outputs
01Prepare input

Structures, ligands, and analysis parameters

02Run analysis

Use a connected research application

03Interpret results

Review molecular evidence and limitations

Experimental complex · Mpro / N3
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The structure can still be examined at RCSB PDB.

RCSB PROTEIN DATA BANK · 6LU7

SARS-CoV-2 main protease

Experimental crystal structure of Mpro in complex with the covalent inhibitor N3.

Ligand
N3 (co-crystallized inhibitor)
Method
X-ray diffraction
Resolution
2.16 Å
Interpretation
Experimentally resolved structure, not a Ligandly docking prediction
View original PDB entry ↗
Experimental Mpro–N3 complex (PDB 6LU7) · Drag to rotate · Scroll to zoom · Internet requiredRCSB PDB ↗
Tools and resources

From molecular questions to testable hypotheses.

Browse research methods and tool access points. Only verified applications should be linked as live services.

01 / COMPUTATION

Molecular docking

Investigate predicted binding poses and compare computational hypotheses.

02 / EVALUATION

Interaction analysis

Examine molecular contacts, residue environments, and interpretation limits.

03 / STRUCTURES

3D visualization

Inspect macromolecular structures in an interactive scientific viewer.

04 / METHODS

Documentation

Understand inputs, outputs, assumptions, and reproducible reporting.

Structure reference

A real protein–ligand complex.

This example uses a single experimentally determined structure, PDB 6LU7, with its co-crystallized inhibitor N3. It does not represent a docking result produced by Ligandly.

01 / STRUCTURE

Mpro–N3 experimental complex

The 6LU7 entry contains SARS-CoV-2 main protease bound to the inhibitor N3. Inspect the full experimental structure in the interactive viewer above.

Open RCSB 3D viewer ↗
02 / LIGAND

N3 · co-crystallized inhibitor

N3 is the ligand associated with this experimental complex. It is not caffeine and is not a ligand independently docked by Ligandly.

Review ligand in source entry ↗
03 / METADATA

Structure details

PDB ID 6LU7
Method X-ray diffraction
Resolution 2.16 Å
Bound inhibitor N3
Source RCSB PDB

Scientific provenance: PDB 6LU7. For reproducible analysis, download the experimental coordinate file from RCSB. No binding-affinity or docking score is asserted here.

Ligandly · Molecular research software

 

Demonstration structure: PDB 6LU7 · Mol*