Ligand profile

2X7

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

Bound to: VK055_2653 — 3,4-dihydroxyphenylacetate 2,3-dioxygenase

Via homolog PDB 3vsj UniProt Q6J1Z6 Formula C₆H₅NO₂
Mol. weight 123.11 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2X7
PDB
3vsj
UniProt (similar protein)
Q6J1Z6
Target protein
VK055_2653

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 123.11 Da
LogP (Crippen) 0.12
H-bond donors 1
H-bond acceptors 3
TPSA 54.06 Ų
Rotatable bonds 0
Aromatic rings 1 / 1
Heavy atoms 9
Fraction sp³ C 0.00
Formula C₆H₅NO₂

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 54.1
  • −1 ≤ LogP ≤ 5 0.12
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 123.1
  • LogP ≤ 5 0.12
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 54.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[H]/N=C/1\C=CC=COC1=O
InChI 
InChI=1S/C6H5NO2/c7-5-3-1-2-4-9-6(5)8/h1-4,7H/b7-5+
InChIKey 
HQPIXVSGYRVKOL-FNORWQNLSA-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

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_2653.

PDB 2

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)