Ligand profile

03I

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

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

Via homolog PDB 3u1y UniProt P47205 Formula C₂₅H₃₄N₂O₆S
Mol. weight 490.62 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
03I
PDB
3u1y
UniProt (similar protein)
P47205
Target protein
VK055_2471

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 490.62 Da
LogP (Crippen) 2.70
H-bond donors 2
H-bond acceptors 7
TPSA 105.17 Ų
Rotatable bonds 11
Aromatic rings 2 / 3
Heavy atoms 34
Fraction sp³ C 0.48
Formula C₂₅H₃₄N₂O₆S

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 105.2
  • −1 ≤ LogP ≤ 5 2.70
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 490.6
  • LogP ≤ 5 2.70
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 105.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@](CCc1ccc(cc1)c2ccc(cc2)OCCCN3CCOCC3)(C(=O)NO)S(=O)(=O)C
InChI 
InChI=1S/C25H34N2O6S/c1-25(24(28)26-29,34(2,30)31)13-12-20-4-6-21(7-5-20)22-8-10-23(11-9-22)33-17-3-14-27-15-18-32-19-16-27/h4-11,29H,3,12-19H2,1-2H3,(H,26,28)/t25-/m1/s1
InChIKey 
GGIDQMXKOSYOHO-RUZDIDTESA-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)