Ligand profile

ASE

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_01630 — tRNA (cmo5U34)-methyltransferase

Via homolog PDB 4a6e UniProt P46597 Formula C₁₂H₁₄N₂O₂
Mol. weight 218.26 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ASE
PDB
4a6e
UniProt (similar protein)
P46597
Target protein
KP13_01630

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 218.26 Da
LogP (Crippen) 1.55
H-bond donors 3
H-bond acceptors 2
TPSA 65.12 Ų
Rotatable bonds 3
Aromatic rings 2 / 2
Heavy atoms 16
Fraction sp³ C 0.25
Formula C₁₂H₁₄N₂O₂

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 65.1
  • −1 ≤ LogP ≤ 5 1.55
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 218.3
  • LogP ≤ 5 1.55
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 65.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)NCCc1c[nH]c2c1cc(cc2)O
InChI 
InChI=1S/C12H14N2O2/c1-8(15)13-5-4-9-7-14-12-3-2-10(16)6-11(9)12/h2-3,6-7,14,16H,4-5H2,1H3,(H,13,15)
InChIKey 
MVAWJSIDNICKHF-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00891

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 2

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)