Ligand profile

A3S

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

Bound to: VK055_0276 — threonine--tRNA ligase

Via homolog PDB 1tky UniProt P0A8M3 Formula C₁₃H₁₉N₇O₅
Mol. weight 353.34 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
A3S
PDB
1tky
UniProt (similar protein)
P0A8M3
Target protein
VK055_0276

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 353.34 Da
LogP (Crippen) -3.54
H-bond donors 6
H-bond acceptors 11
TPSA 194.66 Ų
Rotatable bonds 5
Aromatic rings 2 / 3
Heavy atoms 25
Fraction sp³ C 0.54
Formula C₁₃H₁₉N₇O₅

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 194.7
  • −1 ≤ LogP ≤ 5 -3.54
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 353.3
  • LogP ≤ 5 -3.54
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 194.7
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)[C@H](CO)N)O)N
InChI 
InChI=1S/C13H19N7O5/c14-5(1-21)12(24)19-7-6(2-22)25-13(9(7)23)20-4-18-8-10(15)16-3-17-11(8)20/h3-7,9,13,21-23H,1-2,14H2,(H,19,24)(H2,15,16,17)/t5-,6+,7+,9+,13+/m0/s1
InChIKey 
ITDKSTILAWHDJI-AYEBZEFBSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF07973

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_0276.

PDB 11

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

Ligand PDB entry

ChEMBL 28

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)