Ligand profile

ZINC5553933

Virtual-screening candidate from ZINC.

Bound to: KP13_01630 — tRNA (cmo5U34)-methyltransferase

Via homolog UniProt P46597 Formula C₁₉H₁₈N₂O₃
Tanimoto 0.65
Mol. weight 322.36 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5553933
UniProt (similar protein)
P46597
Tanimoto
0.646
Target protein
KP13_01630

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 322.36 Da
LogP (Crippen) 2.95
H-bond donors 4
H-bond acceptors 3
TPSA 85.35 Ų
Rotatable bonds 5
Aromatic rings 3 / 3
Heavy atoms 24
Fraction sp³ C 0.11
Formula C₁₉H₁₈N₂O₃

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 85.4
  • −1 ≤ LogP ≤ 5 2.95
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 322.4
  • LogP ≤ 5 2.95
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 85.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(/C=C\c1ccc(O)cc1)NCCc1c[nH]c2ccc(O)cc12
InChI 
InChI=1S/C19H18N2O3/c22-15-4-1-13(2-5-15)3-8-19(24)20-10-9-14-12-21-18-7-6-16(23)11-17(14)18/h1-8,11-12,21-23H,9-10H2,(H,20,24)/b8-3-
InChIKey 
WLZPAFGVOWCVMG-BAQGIRSFSA-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)