Ligand profile

GDE

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

Bound to: VK055_0340 — 2,3-dihydroxyphenylpropionate/2, 3-dihydroxicinnamic acid 1,2-dioxygenase

Via homolog PDB 3wr9 UniProt Q5NTE5 Formula C₇H₆O₅
Mol. weight 170.12 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
GDE
PDB
3wr9
UniProt (similar protein)
Q5NTE5
Target protein
VK055_0340

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 170.12 Da
LogP (Crippen) 0.50
H-bond donors 4
H-bond acceptors 4
TPSA 97.99 Ų
Rotatable bonds 1
Aromatic rings 1 / 1
Heavy atoms 12
Fraction sp³ C 0.00
Formula C₇H₆O₅

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 98.0
  • −1 ≤ LogP ≤ 5 0.50
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 170.1
  • LogP ≤ 5 0.50
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 98.0
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 
c1c(cc(c(c1O)O)O)C(=O)O
InChI 
InChI=1S/C7H6O5/c8-4-1-3(7(11)12)2-5(9)6(4)10/h1-2,8-10H,(H,11,12)
InChIKey 
LNTHITQWFMADLM-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
PF02900' 'PF07746

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_0340.

PDB 1

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)