Ligand profile

ZINC80351222

Virtual-screening candidate from ZINC.

Bound to: VK055_3824 — modulator of DNA gyrase family protein

Via homolog UniProt P0AGG8 Formula C₂₄H₃₀N₂O₃
Tanimoto 0.52
Mol. weight 394.52 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC80351222
UniProt (similar protein)
P0AGG8
Tanimoto
0.524
Target protein
VK055_3824

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 394.52 Da
LogP (Crippen) 2.94
H-bond donors 2
H-bond acceptors 3
TPSA 69.64 Ų
Rotatable bonds 7
Aromatic rings 2 / 3
Heavy atoms 29
Fraction sp³ C 0.42
Formula C₂₄H₃₀N₂O₃

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 2.94
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 394.5
  • LogP ≤ 5 2.94
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 69.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)[C@H](NC(=O)C(c1ccccc1)c1ccccc1)C(=O)N1CCC[C@@H]1CO
InChI 
InChI=1S/C24H30N2O3/c1-17(2)22(24(29)26-15-9-14-20(26)16-27)25-23(28)21(18-10-5-3-6-11-18)19-12-7-4-8-13-19/h3-8,10-13,17,20-22,27H,9,14-16H2,1-2H3,(H,25,28)/t20-,22+/m1/s1
InChIKey 
WVVFLXLYMPNREC-IRLDBZIGSA-N

Provenance

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

Method
LigQ sequence
Query
BB2
Homolog
P0AGG8

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_3824.

PDB 1

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

Ligand PDB entry

ZINC 10

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

Compound Similarity (Tanimoto)