Ligand profile

ZINC146568246

Virtual-screening candidate from ZINC.

Bound to: VK055_2065 — cysteine--tRNA ligase

Via homolog UniProt P49589 Formula C₂₅H₂₉N₇O₃
Tanimoto 0.70
Mol. weight 475.55 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC146568246
UniProt (similar protein)
P49589
Tanimoto
0.700
Target protein
VK055_2065

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 475.55 Da
LogP (Crippen) 4.29
H-bond donors 1
H-bond acceptors 9
TPSA 101.59 Ų
Rotatable bonds 9
Aromatic rings 4 / 4
Heavy atoms 35
Fraction sp³ C 0.28
Formula C₂₅H₂₉N₇O₃

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 101.6
  • −1 ≤ LogP ≤ 5 4.29
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 475.6
  • LogP ≤ 5 4.29
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 9
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 101.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1cc(N(C)CCN(C)C)c([N+](=O)[O-])cc1Nc1nccc(-c2cn(C)c3ccccc23)n1
InChI 
InChI=1S/C25H29N7O3/c1-29(2)12-13-30(3)22-15-24(35-5)20(14-23(22)32(33)34)28-25-26-11-10-19(27-25)18-16-31(4)21-9-7-6-8-17(18)21/h6-11,14-16H,12-13H2,1-5H3,(H,26,27,28)
InChIKey 
PKEPAQKEINNCAB-UHFFFAOYSA-N

Provenance

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

Method
LigQ nearest_k
Query
YY3
Homolog
P49589

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_2065.

PDB 1

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)