Ligand profile

ZINC2583383

Virtual-screening candidate from ZINC.

Bound to: VK055_2421 — 2'-5' RNA ligase

Via homolog UniProt P37025 Formula C₁₃H₁₉N₅O₅
Tanimoto 0.72
Mol. weight 325.33 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC2583383
UniProt (similar protein)
P37025
Tanimoto
0.719
Target protein
VK055_2421

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 325.33 Da
LogP (Crippen) -1.31
H-bond donors 3
H-bond acceptors 10
TPSA 137.77 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 23
Fraction sp³ C 0.62
Formula C₁₃H₁₉N₅O₅

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 137.8
  • −1 ≤ LogP ≤ 5 -1.31
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 325.3
  • LogP ≤ 5 -1.31
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 10
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 137.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COCCO[C@H]1[C@@H](O)[C@H](CO)O[C@@H]1n1cnc2c(N)ncnc21
InChI 
InChI=1S/C13H19N5O5/c1-21-2-3-22-10-9(20)7(4-19)23-13(10)18-6-17-8-11(14)15-5-16-12(8)18/h5-7,9-10,13,19-20H,2-4H2,1H3,(H2,14,15,16)/t7-,9-,10-,13-/m0/s1
InChIKey 
PUDXUJRJLRLJIU-PYSAPBNWSA-N

Provenance

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

Method
LigQ nearest_k
Query
2AM
Homolog
P37025

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_2421.

PDB 1

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)