Ligand profile

MEQ

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: VK055_3808 — ribosomal protein L11 methyltransferase

Via homolog PDB 1nv8 UniProt Q9WYV8 Formula C₆H₁₂N₂O₃
Mol. weight 160.17 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
MEQ
PDB
1nv8
UniProt (similar protein)
Q9WYV8
Target protein
VK055_3808

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 160.17 Da
LogP (Crippen) -1.08
H-bond donors 3
H-bond acceptors 3
TPSA 92.42 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 11
Fraction sp³ C 0.67
Formula C₆H₁₂N₂O₃

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 92.4
  • −1 ≤ LogP ≤ 5 -1.08
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 160.2
  • LogP ≤ 5 -1.08
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 92.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CNC(=O)CC[C@@H](C(=O)O)N
InChI 
InChI=1S/C6H12N2O3/c1-8-5(9)3-2-4(7)6(10)11/h4H,2-3,7H2,1H3,(H,8,9)(H,10,11)/t4-/m0/s1
InChIKey 
ONXPDKGXOOORHB-BYPYZUCNSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF05175

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_3808.

PDB 6

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)