Ligand profile

DGD

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 C₅₁H₉₆O₁₅
Mol. weight 949.31 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DGD
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 949.31 Da
LogP (Crippen) 7.61
H-bond donors 7
H-bond acceptors 15
TPSA 231.13 Ų
Rotatable bonds 42
Aromatic rings 0 / 2
Heavy atoms 66
Fraction sp³ C 0.96
Formula C₅₁H₉₆O₁₅

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 231.1
  • −1 ≤ LogP ≤ 5 7.61
Lipinski's Rule of Five Fail 4 violations
  • MW ≤ 500 Da 949.3
  • LogP ≤ 5 7.61
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 42
  • TPSA ≤ 140 Ų 231.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)CO[C@@H]2[C@@H]([C@H]([C@H]([C@H](O2)CO)O)O)O)O)O)O)OC(=O)CCCCCCCCCCCCCCCCC
InChI 
InChI=1S/C51H96O15/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-42(53)61-36-39(64-43(54)34-32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2)37-62-50-49(60)47(58)45(56)41(66-50)38-63-51-48(59)46(57)44(55)40(35-52)65-51/h39-41,44-52,55-60H,3-38H2,1-2H3/t39-,40-,41-,44+,45+,46+,47+,48-,49-,50-,51+/m1/s1
InChIKey 
LDQFLSUQYHBXSX-HXXRYREZSA-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' '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)