Ligand profile

ZINC59364526

Virtual-screening candidate from ZINC.

Bound to: VK055_3755 — 50S ribosomal protein L3

Via homolog UniProt P60438 Formula C₂₁H₂₂N₂O₇
Tanimoto 0.69
Mol. weight 414.41 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC59364526
UniProt (similar protein)
P60438
Tanimoto
0.688
Target protein
VK055_3755

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 414.41 Da
LogP (Crippen) 0.12
H-bond donors 5
H-bond acceptors 8
TPSA 161.39 Ų
Rotatable bonds 2
Aromatic rings 1 / 4
Heavy atoms 30
Fraction sp³ C 0.38
Formula C₂₁H₂₂N₂O₇

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 161.4
  • −1 ≤ LogP ≤ 5 0.12
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 414.4
  • LogP ≤ 5 0.12
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 161.4
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)cccc4C[C@H]3C[C@@H]12
InChI 
InChI=1S/C21H22N2O7/c1-23(2)15-10-7-9-6-8-4-3-5-11(24)12(8)16(25)13(9)18(27)21(10,30)19(28)14(17(15)26)20(22)29/h3-5,9-10,15,24,26-27,30H,6-7H2,1-2H3,(H2,22,29)/t9-,10-,15+,21-/m0/s1
InChIKey 
XDVCLKFLRAWGIT-QJBAFNDPSA-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)