Ligand profile

JCG

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

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

Via homolog PDB 6e54 UniProt P47205 Formula C₂₄H₂₅FN₂O₆S
Mol. weight 488.54 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JCG
PDB
6e54
UniProt (similar protein)
P47205
Target protein
VK055_2471

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 488.54 Da
LogP (Crippen) 2.93
H-bond donors 2
H-bond acceptors 7
TPSA 114.70 Ų
Rotatable bonds 9
Aromatic rings 3 / 3
Heavy atoms 34
Fraction sp³ C 0.25
Formula C₂₄H₂₅FN₂O₆S

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 2.93
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 488.5
  • LogP ≤ 5 2.93
  • 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(cc2F)OCc3ccccc3)(C(=O)NO)S(=O)(=O)C
InChI 
InChI=1S/C24H25FN2O6S/c1-24(23(29)26-30,34(2,31)32)11-13-27-12-10-18(14-22(27)28)20-9-8-19(15-21(20)25)33-16-17-6-4-3-5-7-17/h3-10,12,14-15,30H,11,13,16H2,1-2H3,(H,26,29)/t24-/m1/s1
InChIKey 
RPIBMYVEZQVKQW-XMMPIXPASA-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)