Ligand profile

J1M

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

Bound to: VK055_2471 — UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosaminedeacetylase

Via homolog PDB 6dui UniProt B7UZI4 Formula C₂₄H₂₆N₂O₆S
Mol. weight 470.55 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
J1M
PDB
6dui
UniProt (similar protein)
B7UZI4
Target protein
VK055_2471

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 470.55 Da
LogP (Crippen) 2.79
H-bond donors 2
H-bond acceptors 7
TPSA 114.70 Ų
Rotatable bonds 9
Aromatic rings 3 / 3
Heavy atoms 33
Fraction sp³ C 0.25
Formula C₂₄H₂₆N₂O₆S

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 114.7
  • −1 ≤ LogP ≤ 5 2.79
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 470.5
  • LogP ≤ 5 2.79
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 114.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@](CCN1C=CC(=CC1=O)c2ccc(cc2)OCc3ccccc3)(C(=O)NO)S(=O)(=O)C
InChI 
InChI=1S/C24H26N2O6S/c1-24(23(28)25-29,33(2,30)31)13-15-26-14-12-20(16-22(26)27)19-8-10-21(11-9-19)32-17-18-6-4-3-5-7-18/h3-12,14,16,29H,13,15,17H2,1-2H3,(H,25,28)/t24-/m0/s1
InChIKey 
QNBNKNVSGBGVPV-DEOSSOPVSA-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
PF03331

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_2471.

PDB 40

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

Ligand PDB entry

ChEMBL 100

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)