Ligand profile

ZINC8830752

Virtual-screening candidate from ZINC.

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

Via homolog UniProt Q72GF3 Formula C₁₀H₁₃N₅O₆
Tanimoto 0.63
Mol. weight 299.24 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC8830752
UniProt (similar protein)
Q72GF3
Tanimoto
0.635
Target protein
VK055_1062

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 299.24 Da
LogP (Crippen) -3.39
H-bond donors 6
H-bond acceptors 9
TPSA 179.48 Ų
Rotatable bonds 2
Aromatic rings 2 / 3
Heavy atoms 21
Fraction sp³ C 0.50
Formula C₁₀H₁₃N₅O₆

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 179.5
  • −1 ≤ LogP ≤ 5 -3.39
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 299.2
  • LogP ≤ 5 -3.39
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 179.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1nc2c([nH]c(=O)n2[C@@H]2O[C@@H](CO)[C@@H](O)[C@@H]2O)c(=O)[nH]1
InChI 
InChI=1S/C10H13N5O6/c11-9-13-6-3(7(19)14-9)12-10(20)15(6)8-5(18)4(17)2(1-16)21-8/h2,4-5,8,16-18H,1H2,(H,12,20)(H3,11,13,14,19)/t2-,4+,5-,8+/m0/s1
InChIKey 
FPGSEBKFEJEOSA-WCHFOYDZSA-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)