Ligand profile

HJ2

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

Bound to: VK055_1655 — penicillin-binding protein 6

Via homolog PDB 3bec UniProt P0AEB2 Formula C₁₅H₂₃N₃O₇S
Mol. weight 389.43 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HJ2
PDB
3bec
UniProt (similar protein)
P0AEB2
Target protein
VK055_1655

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 389.43 Da
LogP (Crippen) -0.45
H-bond donors 6
H-bond acceptors 7
TPSA 179.05 Ų
Rotatable bonds 10
Aromatic rings 0 / 1
Heavy atoms 26
Fraction sp³ C 0.60
Formula C₁₅H₂₃N₃O₇S

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 179.0
  • −1 ≤ LogP ≤ 5 -0.45
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 389.4
  • LogP ≤ 5 -0.45
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 179.0
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)O)NC(=O)CCCC[C@@H](C(=O)O)N)C(=O)O
InChI 
InChI=1S/C15H23N3O7S/c1-7-6-26-12(18-10(7)14(22)23)11(15(24)25)17-9(19)5-3-2-4-8(16)13(20)21/h8,11-12,18H,2-6,16H2,1H3,(H,17,19)(H,20,21)(H,22,23)(H,24,25)/t8-,11-,12+/m0/s1
InChIKey 
HJUSKFHSSKMVMT-KPXOXKRLSA-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
PF00768

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 13

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 50

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

Compound Similarity (Tanimoto)