Ligand profile

SQD

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

Bound to: VK055_4847 — NADH:ubiquinone oxidoreductase, membrane subunitL

Via homolog PDB 6khi UniProt Q8DKX9 Formula C₄₁H₇₈O₁₂S
Mol. weight 795.13 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SQD
PDB
6khi
UniProt (similar protein)
Q8DKX9
Target protein
VK055_4847

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 795.13 Da
LogP (Crippen) 8.12
H-bond donors 4
H-bond acceptors 11
TPSA 186.12 Ų
Rotatable bonds 36
Aromatic rings 0 / 1
Heavy atoms 54
Fraction sp³ C 0.95
Formula C₄₁H₇₈O₁₂S

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 186.1
  • −1 ≤ LogP ≤ 5 8.12
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 795.1
  • LogP ≤ 5 8.12
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 36
  • TPSA ≤ 140 Ų 186.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCCCCC(=O)OC[C@H](COC1[C@@H]([C@H]([C@@H]([C@H](O1)CS(=O)(=O)O)O)O)O)OC(=O)CCCCCCCCCCCCCCC
InChI 
InChI=1S/C41H78O12S/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-36(42)50-31-34(32-51-41-40(46)39(45)38(44)35(53-41)33-54(47,48)49)52-37(43)30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h34-35,38-41,44-46H,3-33H2,1-2H3,(H,47,48,49)/t34-,35-,38-,39+,40-,41?/m1/s1
InChIKey 
RVUUQPKXGDTQPG-XJAOGXMPSA-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
PF00146' 'PF00361' 'PF00662' 'PF01010' 'PF10716

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_4847.

PDB 27

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)