Ligand profile

HJ3

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

Bound to: VK055_5052 — DD-carboxypeptidase, penicillin-binding protein 6b

Via homolog PDB 3beb UniProt P0AEB2 Formula C₁₅H₂₅N₃O₆S
Mol. weight 375.45 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HJ3
PDB
3beb
UniProt (similar protein)
P0AEB2
Target protein
VK055_5052

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 375.45 Da
LogP (Crippen) -0.46
H-bond donors 5
H-bond acceptors 7
TPSA 158.82 Ų
Rotatable bonds 10
Aromatic rings 0 / 1
Heavy atoms 25
Fraction sp³ C 0.73
Formula C₁₅H₂₅N₃O₆S

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 158.8
  • −1 ≤ LogP ≤ 5 -0.46
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 375.4
  • LogP ≤ 5 -0.46
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 158.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)CCCC[C@@H](C(=O)O)N)C(=O)O)C
InChI 
InChI=1S/C15H25N3O6S/c1-15(2)11(14(23)24)18-12(25-15)9(7-19)17-10(20)6-4-3-5-8(16)13(21)22/h7-9,11-12,18H,3-6,16H2,1-2H3,(H,17,20)(H,21,22)(H,23,24)/t8-,9+,11-,12+/m0/s1
InChIKey 
AEEFBHZTXIEBJN-BSJXLVFVSA-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_5052.

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)