Ligand profile

ZINC4823537

Virtual-screening candidate from ZINC.

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

Via homolog UniProt Q72GF3 Formula C₁₀H₁₃N₅O₄S
Tanimoto 0.76
Mol. weight 299.31 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4823537
UniProt (similar protein)
Q72GF3
Tanimoto
0.755
Target protein
VK055_1062

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 299.31 Da
LogP (Crippen) -1.32
H-bond donors 5
H-bond acceptors 9
TPSA 142.44 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 20
Fraction sp³ C 0.50
Formula C₁₀H₁₃N₅O₄S

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 142.4
  • −1 ≤ LogP ≤ 5 -1.32
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 299.3
  • LogP ≤ 5 -1.32
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 142.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1ncnc2c1[nH]c(=S)n2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]1O
InChI 
InChI=1S/C10H13N5O4S/c11-7-4-8(13-2-12-7)15(10(20)14-4)9-6(18)5(17)3(1-16)19-9/h2-3,5-6,9,16-18H,1H2,(H,14,20)(H2,11,12,13)/t3-,5+,6-,9+/m0/s1
InChIKey 
QILZVYQRHGBEAR-FULWYAMNSA-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)