Ligand profile

WUB

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

Bound to: KP13_31991 — pyridoxamine 5'-phosphate oxidase

Via homolog PDB 4hmx UniProt Q396C5 Formula C₁₃H₁₂N₂O₂
Mol. weight 228.25 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
WUB
PDB
4hmx
UniProt (similar protein)
Q396C5
Target protein
KP13_31991

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 228.25 Da
LogP (Crippen) 2.21
H-bond donors 2
H-bond acceptors 3
TPSA 61.69 Ų
Rotatable bonds 1
Aromatic rings 1 / 3
Heavy atoms 17
Fraction sp³ C 0.23
Formula C₁₃H₁₂N₂O₂

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 61.7
  • −1 ≤ LogP ≤ 5 2.21
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 228.3
  • LogP ≤ 5 2.21
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 61.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc2c(c1)N[C@H]3[C@@H](CC=CC3=N2)C(=O)O
InChI 
InChI=1S/C13H12N2O2/c16-13(17)8-4-3-7-11-12(8)15-10-6-2-1-5-9(10)14-11/h1-3,5-8,12,15H,4H2,(H,16,17)/t8-,12+/m1/s1
InChIKey 
JMGCBMVXHPNSFZ-PELKAZGASA-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
PF01243' 'PF10590

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_31991.

PDB 1

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

Ligand PDB entry