Ligand profile

ZINC1759385

Virtual-screening candidate from ZINC.

Bound to: KP13_01630 — tRNA (cmo5U34)-methyltransferase

Via homolog UniProt P46597 Formula C₁₃H₁₅N₃O₃
Tanimoto 0.58
Mol. weight 261.28 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC1759385
UniProt (similar protein)
P46597
Tanimoto
0.580
Target protein
KP13_01630

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 261.28 Da
LogP (Crippen) 2.14
H-bond donors 2
H-bond acceptors 3
TPSA 88.03 Ų
Rotatable bonds 5
Aromatic rings 2 / 2
Heavy atoms 19
Fraction sp³ C 0.31
Formula C₁₃H₁₅N₃O₃

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 88.0
  • −1 ≤ LogP ≤ 5 2.14
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 261.3
  • LogP ≤ 5 2.14
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 88.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)NCCCc1c[nH]c2ccc([N+](=O)[O-])cc12
InChI 
InChI=1S/C13H15N3O3/c1-9(17)14-6-2-3-10-8-15-13-5-4-11(16(18)19)7-12(10)13/h4-5,7-8,15H,2-3,6H2,1H3,(H,14,17)
InChIKey 
LSBZBYDADLOAFE-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)