Ligand profile

ZINC1903864090

Virtual-screening candidate from ZINC.

Bound to: VK055_1865 — penicillin-binding protein 2

Via homolog UniProt P0AD65 Formula C₂₁H₃₃N₃O₅S
Tanimoto 0.65
Mol. weight 439.58 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC1903864090
UniProt (similar protein)
P0AD65
Tanimoto
0.649
Target protein
VK055_1865

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 439.58 Da
LogP (Crippen) 2.41
H-bond donors 0
H-bond acceptors 7
TPSA 88.51 Ų
Rotatable bonds 5
Aromatic rings 0 / 3
Heavy atoms 30
Fraction sp³ C 0.81
Formula C₂₁H₃₃N₃O₅S

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 88.5
  • −1 ≤ LogP ≤ 5 2.41
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 439.6
  • LogP ≤ 5 2.41
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 88.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(C)C(=O)OCOC(=O)[C@@H]1N2C(=O)[C@H](N=CN3CCCCCC3)[C@H]2SC1(C)C
InChI 
InChI=1S/C21H33N3O5S/c1-20(2,3)19(27)29-13-28-18(26)15-21(4,5)30-17-14(16(25)24(15)17)22-12-23-10-8-6-7-9-11-23/h12,14-15,17H,6-11,13H2,1-5H3/t14-,15-,17+/m0/s1
InChIKey 
NPGNOVNWUSPMDP-YQQAZPJKSA-N

Provenance

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

Method
LigQ sequence
Query
CHEMBL530
Homolog
P0AD65

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_1865.

PDB 25

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

Ligand PDB entry

ChEMBL 4

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)