Ligand profile

JBG

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

Bound to: VK055_0465 — metallo-beta-lactamase superfamily protein

Via homolog PDB 6m8q UniProt Q9UKF6 Formula C₂₃H₂₇Cl₂N₃O₅
Mol. weight 496.39 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JBG
PDB
6m8q
UniProt (similar protein)
Q9UKF6
Target protein
VK055_0465

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 496.39 Da
LogP (Crippen) 2.75
H-bond donors 3
H-bond acceptors 6
TPSA 102.34 Ų
Rotatable bonds 9
Aromatic rings 2 / 3
Heavy atoms 33
Fraction sp³ C 0.39
Formula C₂₃H₂₇Cl₂N₃O₅

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 102.3
  • −1 ≤ LogP ≤ 5 2.75
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 496.4
  • LogP ≤ 5 2.75
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 102.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN1CCN(CC1)CCOc2c(cc(c(c2Cl)O)C(=O)N[C@@H](Cc3ccccc3)C(=O)O)Cl
InChI 
InChI=1S/C23H27Cl2N3O5/c1-27-7-9-28(10-8-27)11-12-33-21-17(24)14-16(20(29)19(21)25)22(30)26-18(23(31)32)13-15-5-3-2-4-6-15/h2-6,14,18,29H,7-13H2,1H3,(H,26,30)(H,31,32)/t18-/m0/s1
InChIKey 
XEBIFCYTYHBFTB-SFHVURJKSA-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
PF00753' 'PF10996

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_0465.

PDB 1

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)