Ligand profile

ZINC5138417

Virtual-screening candidate from ZINC.

Bound to: VK055_3824 — modulator of DNA gyrase family protein

Via homolog UniProt P0AGG8 Formula C₁₇H₂₉N₃O₆
Tanimoto 0.50
Mol. weight 371.43 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5138417
UniProt (similar protein)
P0AGG8
Tanimoto
0.500
Target protein
VK055_3824

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 371.43 Da
LogP (Crippen) 0.51
H-bond donors 4
H-bond acceptors 5
TPSA 136.04 Ų
Rotatable bonds 9
Aromatic rings 0 / 1
Heavy atoms 26
Fraction sp³ C 0.76
Formula C₁₇H₂₉N₃O₆

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 136.0
  • −1 ≤ LogP ≤ 5 0.51
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 371.4
  • LogP ≤ 5 0.51
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 136.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCC[C@H](CC(=O)NO)C(=O)N1CCC[C@H]1C(=O)N[C@H](C(=O)O)C(C)C
InChI 
InChI=1S/C17H29N3O6/c1-4-6-11(9-13(21)19-26)16(23)20-8-5-7-12(20)15(22)18-14(10(2)3)17(24)25/h10-12,14,26H,4-9H2,1-3H3,(H,18,22)(H,19,21)(H,24,25)/t11-,12+,14+/m1/s1
InChIKey 
QBLFFOHVDMBOPS-DYEKYZERSA-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)