Ligand profile

TPS

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

Bound to: VK055_3099 — thiamine-phosphate pyrophosphorylase

Via homolog PDB 1g4s UniProt P39594 Formula C₁₂H₁₈N₄O₄PS⁺
Mol. weight 345.34 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
TPS
PDB
1g4s
UniProt (similar protein)
P39594
Target protein
VK055_3099

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 345.34 Da
LogP (Crippen) 0.72
H-bond donors 3
H-bond acceptors 6
TPSA 122.44 Ų
Rotatable bonds 6
Aromatic rings 2 / 2
Heavy atoms 22
Fraction sp³ C 0.42
Formula C₁₂H₁₈N₄O₄PS⁺

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 122.4
  • −1 ≤ LogP ≤ 5 0.72
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 345.3
  • LogP ≤ 5 0.72
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 122.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)O
InChI 
InChI=1S/C12H17N4O4PS/c1-8-11(3-4-20-21(17,18)19)22-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,7H,3-4,6H2,1-2H3,(H3-,13,14,15,17,18,19)/p+1
InChIKey 
HZSAJDVWZRBGIF-UHFFFAOYSA-O

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
PF02581

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_3099.

PDB 9

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)