Ligand profile

ZINC98087485

Virtual-screening candidate from ZINC.

Bound to: VK055_4362 — 5'-3' exonuclease, C-terminal SAM fold family protein

Via homolog UniProt Q8X6R9 Formula C₁₂H₂₀O₄
Tanimoto 0.53
Mol. weight 228.29 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC98087485
UniProt (similar protein)
Q8X6R9
Tanimoto
0.533
Target protein
VK055_4362

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 228.29 Da
LogP (Crippen) 2.54
H-bond donors 2
H-bond acceptors 2
TPSA 74.60 Ų
Rotatable bonds 2
Aromatic rings 0 / 0
Heavy atoms 16
Fraction sp³ C 0.67
Formula C₁₂H₂₀O₄

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 74.6
  • −1 ≤ LogP ≤ 5 2.54
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 228.3
  • LogP ≤ 5 2.54
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 74.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(C)/C(C(=O)O)=C(\C(=O)O)C(C)(C)C
InChI 
InChI=1S/C12H20O4/c1-11(2,3)7(9(13)14)8(10(15)16)12(4,5)6/h1-6H3,(H,13,14)(H,15,16)/b8-7+
InChIKey 
LRWOKNIDORCOJJ-BQYQJAHWSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
PIV
Homolog
Q8X6R9

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_4362.

PDB 2

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

Ligand PDB entry

ZINC 12

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

Compound Similarity (Tanimoto)