Ligand profile

ZINC43543817

Virtual-screening candidate from ZINC.

Bound to: VK055_2604 — 16S rRNA m2G1207 methyltransferase

Via homolog UniProt Q2MG72 Formula C₂₀H₄₀N₄O₁₀
Tanimoto 1.00
Mol. weight 496.56 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC43543817
UniProt (similar protein)
Q2MG72
Tanimoto
1.000
Target protein
VK055_2604

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 496.56 Da
LogP (Crippen) -5.61
H-bond donors 10
H-bond acceptors 14
TPSA 248.39 Ų
Rotatable bonds 6
Aromatic rings 0 / 3
Heavy atoms 34
Fraction sp³ C 1.00
Formula C₂₀H₄₀N₄O₁₀

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 248.4
  • −1 ≤ LogP ≤ 5 -5.61
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 496.6
  • LogP ≤ 5 -5.61
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 248.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN[C@@H]1[C@@H](O)[C@@H](O[C@@H]2[C@@H](O)[C@H](O[C@H]3O[C@H]([C@@H](C)O)[C@@H](O)[C@H](O)[C@H]3N)[C@@H](N)C[C@H]2N)OC[C@]1(C)O
InChI 
InChI=1S/C20H40N4O10/c1-6(25)14-11(27)10(26)9(23)18(32-14)33-15-7(21)4-8(22)16(12(15)28)34-19-13(29)17(24-3)20(2,30)5-31-19/h6-19,24-30H,4-5,21-23H2,1-3H3/t6-,7+,8-,9-,10-,11+,12+,13-,14-,15-,16+,17-,18-,19-,20+/m1/s1
InChIKey 
BRZYSWJRSDMWLG-DJWUNRQOSA-N

Provenance

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

Method
LigQ nearest_k
Query
GET
Homolog
Q2MG72

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_2604.

PDB 5

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)