Ligand profile

63U

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: VK055_2402 — penicillin-binding protein 1B

Via homolog PDB 5hla UniProt P02919 Formula C₁₆H₁₉N₃O₄S
Mol. weight 349.41 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
63U
PDB
5hla
UniProt (similar protein)
P02919
Target protein
VK055_2402

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 349.41 Da
LogP (Crippen) 0.39
H-bond donors 4
H-bond acceptors 6
TPSA 121.52 Ų
Rotatable bonds 6
Aromatic rings 1 / 2
Heavy atoms 24
Fraction sp³ C 0.31
Formula C₁₆H₁₉N₃O₄S

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 121.5
  • −1 ≤ LogP ≤ 5 0.39
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 349.4
  • LogP ≤ 5 0.39
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 121.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1=C(N[C@@H](SC1)[C@@H](C=O)NC(=O)[C@@H](c2ccccc2)N)C(=O)O
InChI 
InChI=1S/C16H19N3O4S/c1-9-8-24-15(19-13(9)16(22)23)11(7-20)18-14(21)12(17)10-5-3-2-4-6-10/h2-7,11-12,15,19H,8,17H2,1H3,(H,18,21)(H,22,23)/t11-,12-,15+/m1/s1
InChIKey 
YUNPQAOWKVWRNR-JMSVASOKSA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00905

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_2402.

PDB 11

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)