Ligand profile

SAR

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

Bound to: KP13_04940 — N-methyl-L-tryptophan oxidase

Via homolog PDB 3qse UniProt P40859 Formula C₃H₇NO₂
Mol. weight 89.09 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SAR
PDB
3qse
UniProt (similar protein)
P40859
Target protein
KP13_04940

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 89.09 Da
LogP (Crippen) -0.71
H-bond donors 2
H-bond acceptors 2
TPSA 49.33 Ų
Rotatable bonds 2
Aromatic rings 0 / 0
Heavy atoms 6
Fraction sp³ C 0.67
Formula C₃H₇NO₂

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 49.3
  • −1 ≤ LogP ≤ 5 -0.71
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 89.1
  • LogP ≤ 5 -0.71
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 49.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CNCC(=O)O
InChI 
InChI=1S/C3H7NO2/c1-4-2-3(5)6/h4H,2H2,1H3,(H,5,6)
InChIKey 
FSYKKLYZXJSNPZ-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
PF01266

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_04940.

PDB 10

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)