Ligand profile

QGD

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

Bound to: VK055_2909 — mechanosensitive ion channel family protein

Via homolog PDB 6urt UniProt P0AEB5 Formula C₄₀H₈₀NO₉P
Mol. weight 750.05 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
QGD
PDB
6urt
UniProt (similar protein)
P0AEB5
Target protein
VK055_2909

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 750.05 Da
LogP (Crippen) 11.20
H-bond donors 3
H-bond acceptors 8
TPSA 154.61 Ų
Rotatable bonds 41
Aromatic rings 0 / 0
Heavy atoms 51
Fraction sp³ C 0.95
Formula C₄₀H₈₀NO₉P

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 154.6
  • −1 ≤ LogP ≤ 5 11.20
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 750.1
  • LogP ≤ 5 11.20
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 41
  • TPSA ≤ 140 Ų 154.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCCCCCCCCCOC[C@H](COP(=O)(O)OC[C@@H](C(=O)O)N)OC(=O)CCCCCCCCCCCCC
InChI 
InChI=1S/C40H80NO9P/c1-3-5-7-9-11-13-15-16-17-18-19-20-21-23-25-27-29-31-33-47-34-37(35-48-51(45,46)49-36-38(41)40(43)44)50-39(42)32-30-28-26-24-22-14-12-10-8-6-4-2/h37-38H,3-36,41H2,1-2H3,(H,43,44)(H,45,46)/t37-,38+/m1/s1
InChIKey 
FQGGGDDJZMNTTN-AMAPPZPBSA-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
PF21088

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_2909.

PDB 6

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)