Ligand profile

ZINC54053589

Virtual-screening candidate from ZINC.

Bound to: VK055_1655 — penicillin-binding protein 6

Via homolog UniProt P08506 Formula C₁₆H₁₇N₅O₄S
Tanimoto 0.71
Mol. weight 375.41 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC54053589
UniProt (similar protein)
P08506
Tanimoto
0.714
Target protein
VK055_1655

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 375.41 Da
LogP (Crippen) 1.67
H-bond donors 2
H-bond acceptors 5
TPSA 135.47 Ų
Rotatable bonds 5
Aromatic rings 1 / 3
Heavy atoms 26
Fraction sp³ C 0.44
Formula C₁₆H₁₇N₅O₄S

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 135.5
  • −1 ≤ LogP ≤ 5 1.67
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 375.4
  • LogP ≤ 5 1.67
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 135.5
PAINS Alert

Matches PAINS filter: azo_A(324). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1(C)S[C@@H]2[C@H](NC(=O)[C@H](N=[N+]=[N-])c3ccccc3)C(=O)N2[C@@H]1C(=O)O
InChI 
InChI=1S/C16H17N5O4S/c1-16(2)11(15(24)25)21-13(23)10(14(21)26-16)18-12(22)9(19-20-17)8-6-4-3-5-7-8/h3-7,9-11,14H,1-2H3,(H,18,22)(H,24,25)/t9-,10-,11-,14-/m1/s1
InChIKey 
ODFHGIPNGIAMDK-ZHSDAYTOSA-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)