Ligand profile

A3G

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: VK055_3290 — D-tyrosyl-tRNA(Tyr) deacylase

Via homolog PDB 5j61 UniProt Q8IIS0 Formula C₁₂H₁₇N₇O₄
Mol. weight 323.31 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
A3G
PDB
5j61
UniProt (similar protein)
Q8IIS0
Target protein
VK055_3290

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 323.31 Da
LogP (Crippen) -2.90
H-bond donors 5
H-bond acceptors 10
TPSA 174.43 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 23
Fraction sp³ C 0.50
Formula C₁₂H₁₇N₇O₄

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 174.4
  • −1 ≤ LogP ≤ 5 -2.90
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 323.3
  • LogP ≤ 5 -2.90
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 174.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)NC(=O)CN)O)N
InChI 
InChI=1S/C12H17N7O4/c13-1-6(21)18-7-5(2-20)23-12(9(7)22)19-4-17-8-10(14)15-3-16-11(8)19/h3-5,7,9,12,20,22H,1-2,13H2,(H,18,21)(H2,14,15,16)/t5-,7-,9-,12-/m1/s1
InChIKey 
XJJYXFHVLHMVGL-MUIQIWNUSA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF02580

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_3290.

PDB 3

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)