Ligand profile

ZINC2496147

Virtual-screening candidate from ZINC.

Bound to: KP13_01630 — tRNA (cmo5U34)-methyltransferase

Via homolog UniProt P46597 Formula C₁₉H₂₀N₂O₂
Tanimoto 0.64
Mol. weight 308.38 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC2496147
UniProt (similar protein)
P46597
Tanimoto
0.640
Target protein
KP13_01630

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 308.38 Da
LogP (Crippen) 3.43
H-bond donors 2
H-bond acceptors 2
TPSA 54.12 Ų
Rotatable bonds 6
Aromatic rings 3 / 3
Heavy atoms 23
Fraction sp³ C 0.21
Formula C₁₉H₂₀N₂O₂

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 54.1
  • −1 ≤ LogP ≤ 5 3.43
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 308.4
  • LogP ≤ 5 3.43
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 54.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)NCCc1c[nH]c2ccc(OCc3ccccc3)cc12
InChI 
InChI=1S/C19H20N2O2/c1-14(22)20-10-9-16-12-21-19-8-7-17(11-18(16)19)23-13-15-5-3-2-4-6-15/h2-8,11-12,21H,9-10,13H2,1H3,(H,20,22)
InChIKey 
NYFDZJCKTLWFCP-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
ASE
Homolog
P46597

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_01630.

PDB 3

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)