Ligand profile

ZINC17064639

Virtual-screening candidate from ZINC.

Bound to: VK055_1062 — ATP-dependent RNA helicase, specific for 23S rRNA

Via homolog UniProt Q72GF3 Formula C₁₃H₁₅N₇O₅
Tanimoto 0.61
Mol. weight 349.31 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC17064639
UniProt (similar protein)
Q72GF3
Tanimoto
0.614
Target protein
VK055_1062

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 349.31 Da
LogP (Crippen) -2.56
H-bond donors 6
H-bond acceptors 11
TPSA 198.42 Ų
Rotatable bonds 2
Aromatic rings 3 / 4
Heavy atoms 25
Fraction sp³ C 0.38
Formula C₁₃H₁₅N₇O₅

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 198.4
  • −1 ≤ LogP ≤ 5 -2.56
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 349.3
  • LogP ≤ 5 -2.56
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 198.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1nc(=O)c2c3c(N)ncnc3n([C@@H]3O[C@@H](CO)[C@@H](O)[C@@H]3O)c2[nH]1
InChI 
InChI=1S/C13H15N7O5/c14-8-4-5-10(18-13(15)19-11(5)24)20(9(4)17-2-16-8)12-7(23)6(22)3(1-21)25-12/h2-3,6-7,12,21-23H,1H2,(H2,14,16,17)(H3,15,18,19,24)/t3-,6+,7-,12+/m0/s1
InChIKey 
SNKLMUGPSNINBD-GTWRCXMXSA-N

Provenance

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

Method
LigQ nearest_k
Query
8OX
Homolog
Q72GF3

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_1062.

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)