Ligand profile

DNA

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

Bound to: VK055_4853 — 2-succinyl-5-enolpyruvyl-6-hydroxy-3- cyclohexene-1-carboxylic-acid synthase

Via homolog PDB 6o0j UniProt P9WK11 Formula C₁₁H₈O₄
Mol. weight 204.18 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DNA
PDB
6o0j
UniProt (similar protein)
P9WK11
Target protein
VK055_4853

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 204.18 Da
LogP (Crippen) 1.95
H-bond donors 3
H-bond acceptors 3
TPSA 77.76 Ų
Rotatable bonds 1
Aromatic rings 2 / 2
Heavy atoms 15
Fraction sp³ C 0.00
Formula C₁₁H₈O₄

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 77.8
  • −1 ≤ LogP ≤ 5 1.95
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 204.2
  • LogP ≤ 5 1.95
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 77.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc2c(c1)c(cc(c2O)C(=O)O)O
InChI 
InChI=1S/C11H8O4/c12-9-5-8(11(14)15)10(13)7-4-2-1-3-6(7)9/h1-5,12-13H,(H,14,15)
InChIKey 
VOJUXHHACRXLTD-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
PF02776

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_4853.

PDB 5

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

Ligand PDB entry

ChEMBL 2

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)