Ligand profile

PBO

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

Bound to: KP13_05032 — Methylated-DNA--protein-cysteine methyltransferase

Via homolog PDB 3gyh UniProt Q9UTN9 Formula C₉H₁₁NO
Mol. weight 149.19 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PBO
PDB
3gyh
UniProt (similar protein)
Q9UTN9
Target protein
KP13_05032

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 149.19 Da
LogP (Crippen) 2.06
H-bond donors 0
H-bond acceptors 2
TPSA 29.96 Ų
Rotatable bonds 3
Aromatic rings 1 / 1
Heavy atoms 11
Fraction sp³ C 0.33
Formula C₉H₁₁NO

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 30.0
  • −1 ≤ LogP ≤ 5 2.06
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 149.2
  • LogP ≤ 5 2.06
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 30.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCC(=O)c1cccnc1
InChI 
InChI=1S/C9H11NO/c1-2-4-9(11)8-5-3-6-10-7-8/h3,5-7H,2,4H2,1H3
InChIKey 
JORUAYHMUWRFNM-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
PF01035

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_05032.

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)