Ligand profile

ZINC2382315467

Virtual-screening candidate from ZINC.

Bound to: VK055_3755 — 50S ribosomal protein L3

Via homolog UniProt P60438 Formula C₂₁H₂₂N₂O₈
Tanimoto 0.70
Mol. weight 430.41 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC2382315467
UniProt (similar protein)
P60438
Tanimoto
0.698
Target protein
VK055_3755

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 430.41 Da
LogP (Crippen) -0.39
H-bond donors 6
H-bond acceptors 9
TPSA 181.62 Ų
Rotatable bonds 2
Aromatic rings 1 / 4
Heavy atoms 31
Fraction sp³ C 0.38
Formula C₂₁H₂₂N₂O₈

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 181.6
  • −1 ≤ LogP ≤ 5 -0.39
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 430.4
  • LogP ≤ 5 -0.39
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 181.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@]2(O)C(O)=C3C(=O)c4c(O)cccc4[C@@H](O)[C@H]3C[C@@H]12
InChI 
InChI=1S/C21H22N2O8/c1-23(2)14-9-6-8-12(16(26)11-7(15(8)25)4-3-5-10(11)24)18(28)21(9,31)19(29)13(17(14)27)20(22)30/h3-5,8-9,14-15,24-25,27-28,31H,6H2,1-2H3,(H2,22,30)/t8-,9-,14-,15+,21+/m0/s1
InChIKey 
JCSGAUKCDAVARS-ASYXJBQNSA-N

Provenance

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

Method
LigQ sequence
Query
TAC
Homolog
P60438

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_3755.

PDB 6

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)