Ligand profile

ZINC2325785154

Virtual-screening candidate from ZINC.

Bound to: KP13_01630 — tRNA (cmo5U34)-methyltransferase

Via homolog UniProt P46597 Formula C₁₉H₂₈N₄O₂
Tanimoto 0.60
Mol. weight 344.46 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC2325785154
UniProt (similar protein)
P46597
Tanimoto
0.604
Target protein
KP13_01630

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 344.46 Da
LogP (Crippen) 2.64
H-bond donors 5
H-bond acceptors 3
TPSA 89.18 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 25
Fraction sp³ C 0.53
Formula C₁₉H₂₈N₄O₂

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 89.2
  • −1 ≤ LogP ≤ 5 2.64
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 344.5
  • LogP ≤ 5 2.64
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 89.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CNC1(CNC(=O)NCCc2c[nH]c3ccc(O)cc23)CCCCC1
InChI 
InChI=1S/C19H28N4O2/c1-20-19(8-3-2-4-9-19)13-23-18(25)21-10-7-14-12-22-17-6-5-15(24)11-16(14)17/h5-6,11-12,20,22,24H,2-4,7-10,13H2,1H3,(H2,21,23,25)
InChIKey 
FWXMDNQPEBOSSF-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)