Ligand profile

ZINC2386269587

Virtual-screening candidate from ZINC.

Bound to: VK055_0586 — bacterial extracellular solute-binding, 3 familyprotein

Via homolog UniProt Q7D447 Formula C₁₂H₂₄N₂O₇
Tanimoto 0.73
Mol. weight 308.33 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC2386269587
UniProt (similar protein)
Q7D447
Tanimoto
0.729
Target protein
VK055_0586

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 308.33 Da
LogP (Crippen) -3.04
H-bond donors 7
H-bond acceptors 8
TPSA 165.50 Ų
Rotatable bonds 8
Aromatic rings 0 / 1
Heavy atoms 21
Fraction sp³ C 0.92
Formula C₁₂H₂₄N₂O₇

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

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 165.5
  • −1 ≤ LogP ≤ 5 -3.04
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 308.3
  • LogP ≤ 5 -3.04
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 165.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
NCCCC[C@H](NC[C@@]1(O)OC[C@@H](O)[C@@H](O)[C@@H]1O)C(=O)O
InChI 
InChI=1S/C12H24N2O7/c13-4-2-1-3-7(11(18)19)14-6-12(20)10(17)9(16)8(15)5-21-12/h7-10,14-17,20H,1-6,13H2,(H,18,19)/t7-,8+,9+,10-,12+/m0/s1
InChIKey 
MJTOFLFMNGKVNS-TYCYOEEFSA-N

Provenance

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

Method
LigQ nearest_k
Query
SNW
Homolog
Q7D447

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_0586.

PDB 2

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

Ligand PDB entry

ZINC 47

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

Compound Similarity (Tanimoto)