Ligand profile

ZINC4899869

Virtual-screening candidate from ZINC.

Bound to: VK055_1868 — penicillin-binding protein 6

Via homolog UniProt P0AEB2 Formula C₁₆H₂₂N₂O₆
Tanimoto 0.63
Mol. weight 338.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4899869
UniProt (similar protein)
P0AEB2
Tanimoto
0.629
Target protein
VK055_1868

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 338.36 Da
LogP (Crippen) 1.89
H-bond donors 3
H-bond acceptors 5
TPSA 113.96 Ų
Rotatable bonds 9
Aromatic rings 1 / 1
Heavy atoms 24
Fraction sp³ C 0.44
Formula C₁₆H₂₂N₂O₆

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 114.0
  • −1 ≤ LogP ≤ 5 1.89
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 338.4
  • LogP ≤ 5 1.89
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 114.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COC(=O)N[C@@H](CCCCNC(=O)OCc1ccccc1)C(=O)O
InChI 
InChI=1S/C16H22N2O6/c1-23-16(22)18-13(14(19)20)9-5-6-10-17-15(21)24-11-12-7-3-2-4-8-12/h2-4,7-8,13H,5-6,9-11H2,1H3,(H,17,21)(H,18,22)(H,19,20)/t13-/m0/s1
InChIKey 
YBHGRGORRMOMMY-ZDUSSCGKSA-N

Provenance

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

Method
LigQ sequence
Query
BO9
Homolog
P0AEB2

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_1868.

PDB 15

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

Ligand PDB entry

ChEMBL 1

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 49

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

Compound Similarity (Tanimoto)