Ligand profile

ZINC38778809

Virtual-screening candidate from ZINC.

Bound to: KP13_01630 — tRNA (cmo5U34)-methyltransferase

Via homolog UniProt P46597 Formula C₁₅H₂₀N₂O₃
Tanimoto 0.71
Mol. weight 276.34 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC38778809
UniProt (similar protein)
P46597
Tanimoto
0.711
Target protein
KP13_01630

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 276.34 Da
LogP (Crippen) 2.94
H-bond donors 3
H-bond acceptors 3
TPSA 74.35 Ų
Rotatable bonds 3
Aromatic rings 2 / 2
Heavy atoms 20
Fraction sp³ C 0.40
Formula C₁₅H₂₀N₂O₃

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 74.3
  • −1 ≤ LogP ≤ 5 2.94
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 276.3
  • LogP ≤ 5 2.94
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 74.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(C)OC(=O)NCCc1c[nH]c2ccc(O)cc12
InChI 
InChI=1S/C15H20N2O3/c1-15(2,3)20-14(19)16-7-6-10-9-17-13-5-4-11(18)8-12(10)13/h4-5,8-9,17-18H,6-7H2,1-3H3,(H,16,19)
InChIKey 
IIMONFHUAYVZPV-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)