Ligand profile

VNL

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

Bound to: VK055_3046 — chorismate lyase

Via homolog PDB 1xlr UniProt P26602 Formula C₈H₇O₄⁻
Mol. weight 167.14 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
VNL
PDB
1xlr
UniProt (similar protein)
P26602
Target protein
VK055_3046

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 167.14 Da
LogP (Crippen) -0.24
H-bond donors 1
H-bond acceptors 4
TPSA 69.59 Ų
Rotatable bonds 2
Aromatic rings 1 / 1
Heavy atoms 12
Fraction sp³ C 0.12
Formula C₈H₇O₄⁻

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 69.6
  • −1 ≤ LogP ≤ 5 -0.24
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 167.1
  • LogP ≤ 5 -0.24
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 69.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1cc(ccc1O)C(=O)[O-]
InChI 
InChI=1S/C8H8O4/c1-12-7-4-5(8(10)11)2-3-6(7)9/h2-4,9H,1H3,(H,10,11)/p-1
InChIKey 
WKOLLVMJNQIZCI-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
PF04345

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_3046.

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)