Ligand profile

ZINC1507230

Virtual-screening candidate from ZINC.

Bound to: KP13_01630 — tRNA (cmo5U34)-methyltransferase

Via homolog UniProt P46597 Formula C₁₆H₁₉N₃O₃
Tanimoto 0.57
Mol. weight 301.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC1507230
UniProt (similar protein)
P46597
Tanimoto
0.574
Target protein
KP13_01630

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 301.35 Da
LogP (Crippen) 1.06
H-bond donors 4
H-bond acceptors 3
TPSA 94.22 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 22
Fraction sp³ C 0.38
Formula C₁₆H₁₉N₃O₃

Drug-likeness

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

Permeability proxy Check

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 94.2
  • −1 ≤ LogP ≤ 5 1.06
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 301.3
  • LogP ≤ 5 1.06
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 94.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C1NCCC[C@H]1C(=O)NCCc1c[nH]c2ccc(O)cc12
InChI 
InChI=1S/C16H19N3O3/c20-11-3-4-14-13(8-11)10(9-19-14)5-7-18-16(22)12-2-1-6-17-15(12)21/h3-4,8-9,12,19-20H,1-2,5-7H2,(H,17,21)(H,18,22)/t12-/m1/s1
InChIKey 
ZIMKJLALTRLXJO-GFCCVEGCSA-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)