Ligand profile

DST

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

Bound to: VK055_2895 — tRNA dimethylallyltransferase

Via homolog PDB 2zxu UniProt P16384 Formula C₅H₁₂O₆P₂S
Mol. weight 262.16 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DST
PDB
2zxu
UniProt (similar protein)
P16384
Target protein
VK055_2895

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 262.16 Da
LogP (Crippen) 1.90
H-bond donors 3
H-bond acceptors 4
TPSA 104.06 Ų
Rotatable bonds 5
Aromatic rings 0 / 0
Heavy atoms 14
Fraction sp³ C 0.60
Formula C₅H₁₂O₆P₂S

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 104.1
  • −1 ≤ LogP ≤ 5 1.90
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 262.2
  • LogP ≤ 5 1.90
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 104.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=CCS[P@@](=O)(O)OP(=O)(O)O)C
InChI 
InChI=1S/C5H12O6P2S/c1-5(2)3-4-14-13(9,10)11-12(6,7)8/h3H,4H2,1-2H3,(H,9,10)(H2,6,7,8)
InChIKey 
ZWFWSISPSBLNGO-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF01715

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_2895.

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)