Ligand profile

PYC

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

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

Via homolog PDB 1eli UniProt P40859 Formula C₅H₄NO₂⁻
Mol. weight 110.09 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PYC
PDB
1eli
UniProt (similar protein)
P40859
Target protein
KP13_04940

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 110.09 Da
LogP (Crippen) -0.62
H-bond donors 1
H-bond acceptors 2
TPSA 55.92 Ų
Rotatable bonds 1
Aromatic rings 1 / 1
Heavy atoms 8
Fraction sp³ C 0.00
Formula C₅H₄NO₂⁻

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 55.9
  • −1 ≤ LogP ≤ 5 -0.62
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 110.1
  • LogP ≤ 5 -0.62
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 55.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc([nH]c1)C(=O)[O-]
InChI 
InChI=1S/C5H5NO2/c7-5(8)4-2-1-3-6-4/h1-3,6H,(H,7,8)/p-1
InChIKey 
WRHZVMBBRYBTKZ-UHFFFAOYSA-M

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)