Ligand profile

VDO

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

Bound to: VK055_0055 — alpha,alpha-trehalose-phosphate synthase

Via homolog PDB 2wtx UniProt P31677 Formula C₁₄H₂₆NO₁₁P
Mol. weight 415.33 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
VDO
PDB
2wtx
UniProt (similar protein)
P31677
Target protein
VK055_0055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 415.33 Da
LogP (Crippen) -4.46
H-bond donors 10
H-bond acceptors 10
TPSA 220.40 Ų
Rotatable bonds 6
Aromatic rings 0 / 2
Heavy atoms 27
Fraction sp³ C 0.86
Formula C₁₄H₂₆NO₁₁P

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 220.4
  • −1 ≤ LogP ≤ 5 -4.46
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 415.3
  • LogP ≤ 5 -4.46
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 220.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@@H]([C@H]([C@@H]([C@H]([C@H]1N[C@H]2C=C([C@H]([C@@H]([C@H]2O)O)O)CO)O)O)O)COP(=O)(O)O
InChI 
InChI=1S/C14H26NO11P/c16-3-5-1-7(11(19)13(21)9(5)17)15-8-2-6(4-26-27(23,24)25)10(18)14(22)12(8)20/h1,6-22H,2-4H2,(H2,23,24,25)/t6-,7+,8+,9-,10-,11+,12+,13+,14+/m1/s1
InChIKey 
ZKSTYMJGEHZSFH-MBABXGOBSA-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
PF00982

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_0055.

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)