Ligand profile

ZINC5390315

Virtual-screening candidate from ZINC.

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

Via homolog UniProt Q72GF3 Formula C₁₃H₁₄N₆O₆
Tanimoto 0.64
Mol. weight 350.29 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5390315
UniProt (similar protein)
Q72GF3
Tanimoto
0.643
Target protein
VK055_1062

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 350.29 Da
LogP (Crippen) -2.85
H-bond donors 6
H-bond acceptors 10
TPSA 192.37 Ų
Rotatable bonds 2
Aromatic rings 3 / 4
Heavy atoms 25
Fraction sp³ C 0.38
Formula C₁₃H₁₄N₆O₆

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 192.4
  • −1 ≤ LogP ≤ 5 -2.85
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 350.3
  • LogP ≤ 5 -2.85
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 192.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1ncnc2c1c1c(=O)[nH]c(=O)[nH]c1n2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]1O
InChI 
InChI=1S/C13H14N6O6/c14-8-4-5-10(17-13(24)18-11(5)23)19(9(4)16-2-15-8)12-7(22)6(21)3(1-20)25-12/h2-3,6-7,12,20-22H,1H2,(H2,14,15,16)(H2,17,18,23,24)/t3-,6+,7-,12+/m0/s1
InChIKey 
PCAZZGMLVCFODV-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)