Ligand profile

ZINC3776540

Virtual-screening candidate from ZINC.

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

Via homolog UniProt P37025 Formula C₁₁H₁₅N₅O₄
Tanimoto 0.74
Mol. weight 281.27 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC3776540
UniProt (similar protein)
P37025
Tanimoto
0.741
Target protein
VK055_2421

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 281.27 Da
LogP (Crippen) -1.33
H-bond donors 3
H-bond acceptors 9
TPSA 128.54 Ų
Rotatable bonds 3
Aromatic rings 2 / 3
Heavy atoms 20
Fraction sp³ C 0.55
Formula C₁₁H₁₅N₅O₄

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 128.5
  • −1 ≤ LogP ≤ 5 -1.33
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 281.3
  • LogP ≤ 5 -1.33
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 9
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 128.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CO[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1n1cnc2c(N)ncnc21
InChI 
InChI=1S/C11H15N5O4/c1-19-8-7(18)5(2-17)20-11(8)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H2,12,13,14)/t5-,7-,8-,11-/m1/s1
InChIKey 
FPUGCISOLXNPPC-IOSLPCCCSA-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)