Ligand profile

ZINC39205441

Virtual-screening candidate from ZINC.

Bound to: VK055_0947 — malonate decarboxylase, epsilon subunit

Via homolog UniProt Q9KQH6 Formula C₁₃H₂₂O₅
Tanimoto 0.62
Mol. weight 258.31 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC39205441
UniProt (similar protein)
Q9KQH6
Tanimoto
0.625
Target protein
VK055_0947

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 258.31 Da
LogP (Crippen) 2.02
H-bond donors 0
H-bond acceptors 5
TPSA 69.67 Ų
Rotatable bonds 10
Aromatic rings 0 / 0
Heavy atoms 18
Fraction sp³ C 0.77
Formula C₁₃H₂₂O₅

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 69.7
  • −1 ≤ LogP ≤ 5 2.02
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 258.3
  • LogP ≤ 5 2.02
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 69.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCOC(=O)CC(=O)CC(=O)OCCCC
InChI 
InChI=1S/C13H22O5/c1-3-5-7-17-12(15)9-11(14)10-13(16)18-8-6-4-2/h3-10H2,1-2H3
InChIKey 
SAPPVGOXJLSDHG-UHFFFAOYSA-N

Provenance

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

Method
LigQ nearest_k
Query
8JZ
Homolog
Q9KQH6

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_0947.

PDB 10

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)