Ligand profile

3WL

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

Bound to: KP13_05149 — Lactoylglutathione lyase

Via homolog PDB 4x2a UniProt Q9CPU0 Formula C₁₅H₁₀O₅
Mol. weight 270.24 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
3WL
PDB
4x2a
UniProt (similar protein)
Q9CPU0
Target protein
KP13_05149

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 270.24 Da
LogP (Crippen) 2.58
H-bond donors 3
H-bond acceptors 5
TPSA 90.90 Ų
Rotatable bonds 1
Aromatic rings 3 / 3
Heavy atoms 20
Fraction sp³ C 0.00
Formula C₁₅H₁₀O₅

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

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 90.9
  • −1 ≤ LogP ≤ 5 2.58
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 270.2
  • LogP ≤ 5 2.58
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 90.9
PAINS Alert

Matches PAINS filter: catechol_A(92). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)C2=CC(=O)c3c(cc(c(c3O)O)O)O2
InChI 
InChI=1S/C15H10O5/c16-9-6-11(8-4-2-1-3-5-8)20-12-7-10(17)14(18)15(19)13(9)12/h1-7,17-19H
InChIKey 
FXNFHKRTJBSTCS-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
PF00903

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_05149.

PDB 15

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

Ligand PDB entry

ChEMBL 61

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)