Ligand profile

ZINC95628425

Virtual-screening candidate from ZINC.

Bound to: KP13_01630 — tRNA (cmo5U34)-methyltransferase

Via homolog UniProt P46597 Formula C₂₁H₁₈N₂O₃
Tanimoto 0.62
Mol. weight 346.39 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC95628425
UniProt (similar protein)
P46597
Tanimoto
0.620
Target protein
KP13_01630

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 346.39 Da
LogP (Crippen) 3.70
H-bond donors 4
H-bond acceptors 3
TPSA 85.35 Ų
Rotatable bonds 4
Aromatic rings 4 / 4
Heavy atoms 26
Fraction sp³ C 0.10
Formula C₂₁H₁₈N₂O₃

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 3.70
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 346.4
  • LogP ≤ 5 3.70
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 85.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(NCCc1c[nH]c2ccc(O)cc12)c1ccc2ccccc2c1O
InChI 
InChI=1S/C21H18N2O3/c24-15-6-8-19-18(11-15)14(12-23-19)9-10-22-21(26)17-7-5-13-3-1-2-4-16(13)20(17)25/h1-8,11-12,23-25H,9-10H2,(H,22,26)
InChIKey 
KHJNISGKGIHTMY-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)