Ligand profile

ZINC4830892

Virtual-screening candidate from ZINC.

Bound to: VK055_0276 — threonine--tRNA ligase

Via homolog UniProt P0A8M3 Formula C₁₁H₁₆N₆O₃
Tanimoto 0.72
Mol. weight 280.29 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4830892
UniProt (similar protein)
P0A8M3
Tanimoto
0.722
Target protein
VK055_0276

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 280.29 Da
LogP (Crippen) -1.75
H-bond donors 4
H-bond acceptors 9
TPSA 131.34 Ų
Rotatable bonds 3
Aromatic rings 2 / 3
Heavy atoms 20
Fraction sp³ C 0.55
Formula C₁₁H₁₆N₆O₃

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 131.3
  • −1 ≤ LogP ≤ 5 -1.75
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 280.3
  • LogP ≤ 5 -1.75
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 9
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 131.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN[C@@H]1[C@H](CO)O[C@H](n2cnc3c(N)ncnc32)[C@@H]1O
InChI 
InChI=1S/C11H16N6O3/c1-13-6-5(2-18)20-11(8(6)19)17-4-16-7-9(12)14-3-15-10(7)17/h3-6,8,11,13,18-19H,2H2,1H3,(H2,12,14,15)/t5-,6+,8+,11-/m0/s1
InChIKey 
ZARAVIBCBGMNJG-NAEKMDOESA-N

Provenance

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

Method
LigQ sequence
Query
A3S
Homolog
P0A8M3

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 12

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 49

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

Compound Similarity (Tanimoto)