Ligand profile

ZINC5426353

Virtual-screening candidate from ZINC.

Bound to: VK055_3770 — ribosomal protein L6

Via homolog UniProt P05738 Formula C₁₂H₂₅N₃O₇
Tanimoto 0.68
Mol. weight 323.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5426353
UniProt (similar protein)
P05738
Tanimoto
0.682
Target protein
VK055_3770

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 323.35 Da
LogP (Crippen) -5.08
H-bond donors 8
H-bond acceptors 10
TPSA 197.67 Ų
Rotatable bonds 3
Aromatic rings 0 / 2
Heavy atoms 22
Fraction sp³ C 1.00
Formula C₁₂H₂₅N₃O₇

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 197.7
  • −1 ≤ LogP ≤ 5 -5.08
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 323.3
  • LogP ≤ 5 -5.08
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 197.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
N[C@H]1C[C@@H](N)[C@H](O[C@H]2O[C@H](CO)[C@@H](O)[C@H](N)[C@H]2O)[C@@H](O)[C@@H]1O
InChI 
InChI=1S/C12H25N3O7/c13-3-1-4(14)11(10(20)7(3)17)22-12-9(19)6(15)8(18)5(2-16)21-12/h3-12,16-20H,1-2,13-15H2/t3-,4+,5+,6-,7+,8+,9+,10-,11-,12+/m0/s1
InChIKey 
WPYNTQYMFOTKRF-OSDBSAJISA-N

Provenance

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

Method
LigQ nearest_k
Query
8UZ
Homolog
P05738

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_3770.

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)