Ligand profile

C0T

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

Bound to: VK055_5103 — Putative UDP-glucoronosyl and UDP-glucosyl transferase

Via homolog PDB 3oti UniProt Q8KND7 Formula C₂₄H₂₈N₂O₉S₃
Mol. weight 584.69 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
C0T
PDB
3oti
UniProt (similar protein)
Q8KND7
Target protein
VK055_5103

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 584.69 Da
LogP (Crippen) 0.66
H-bond donors 6
H-bond acceptors 13
TPSA 166.81 Ų
Rotatable bonds 8
Aromatic rings 0 / 3
Heavy atoms 38
Fraction sp³ C 0.50
Formula C₂₄H₂₈N₂O₉S₃

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 166.8
  • −1 ≤ LogP ≤ 5 0.66
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 584.7
  • LogP ≤ 5 0.66
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 166.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1C(C(C(C(O1)OC2C#CC=CC#CC3(CC(=O)C(=C2C3=CCSSSC)NC(=O)OC)O)O)O)NO
InChI 
InChI=1S/C24H28N2O9S3/c1-13-18(26-32)20(28)21(29)22(34-13)35-16-8-6-4-5-7-10-24(31)12-15(27)19(25-23(30)33-2)17(16)14(24)9-11-37-38-36-3/h4-5,9,13,16,18,20-22,26,28-29,31-32H,11-12H2,1-3H3,(H,25,30)
InChIKey 
HIXBTEQHDWBCIJ-UHFFFAOYSA-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
PF06722' 'PF21036

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_5103.

PDB 4

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)