Ligand profile

ZINC3874216

Virtual-screening candidate from ZINC.

Bound to: VK055_1655 — penicillin-binding protein 6

Via homolog UniProt P08506 Formula C₁₇H₁₉N₃O₄S
Tanimoto 0.75
Mol. weight 361.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC3874216
UniProt (similar protein)
P08506
Tanimoto
0.755
Target protein
VK055_1655

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 361.42 Da
LogP (Crippen) 1.06
H-bond donors 2
H-bond acceptors 5
TPSA 99.07 Ų
Rotatable bonds 5
Aromatic rings 1 / 3
Heavy atoms 25
Fraction sp³ C 0.41
Formula C₁₇H₁₉N₃O₄S

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 99.1
  • −1 ≤ LogP ≤ 5 1.06
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 361.4
  • LogP ≤ 5 1.06
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 99.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C=N[C@@H](C(=O)N[C@@H]1C(=O)N2[C@@H](C(=O)O)C(C)(C)S[C@H]12)c1ccccc1
InChI 
InChI=1S/C17H19N3O4S/c1-17(2)12(16(23)24)20-14(22)11(15(20)25-17)19-13(21)10(18-3)9-7-5-4-6-8-9/h4-8,10-12,15H,3H2,1-2H3,(H,19,21)(H,23,24)/t10-,11-,12+,15-/m1/s1
InChIKey 
FZECHKJQHUVANE-MCYUEQNJSA-N

Provenance

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

Method
LigQ nearest_k
Query
AIC
Homolog
P08506

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_1655.

PDB 14

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)