Ligand profile

ZINC13549616

Virtual-screening candidate from ZINC.

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

Via homolog UniProt P37025 Formula C₁₀H₁₃N₄O₈P
Tanimoto 0.71
Mol. weight 348.21 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC13549616
UniProt (similar protein)
P37025
Tanimoto
0.714
Target protein
VK055_2421

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 348.21 Da
LogP (Crippen) -1.74
H-bond donors 5
H-bond acceptors 10
TPSA 180.28 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 23
Fraction sp³ C 0.50
Formula C₁₀H₁₃N₄O₈P

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 180.3
  • −1 ≤ LogP ≤ 5 -1.74
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 348.2
  • LogP ≤ 5 -1.74
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 180.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=P(O)(O)O[C@@H]1[C@@H](CO)O[C@@H](n2cnc3c(O)ncnc32)[C@@H]1O
InChI 
InChI=1S/C10H13N4O8P/c15-1-4-7(22-23(18,19)20)6(16)10(21-4)14-3-13-5-8(14)11-2-12-9(5)17/h2-4,6-7,10,15-16H,1H2,(H,11,12,17)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKey 
XALREVCCJXUVAL-KQYNXXCUSA-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)