Ligand profile

FTP

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

Bound to: VK055_3099 — thiamine-phosphate pyrophosphorylase

Via homolog PDB 1g4t UniProt P39594 Formula C₁₂H₁₃F₃N₄O₄PS⁻
Mol. weight 397.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
FTP
PDB
1g4t
UniProt (similar protein)
P39594
Target protein
VK055_3099

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 397.30 Da
LogP (Crippen) 0.17
H-bond donors 1
H-bond acceptors 8
TPSA 128.10 Ų
Rotatable bonds 6
Aromatic rings 2 / 2
Heavy atoms 25
Fraction sp³ C 0.42
Formula C₁₂H₁₃F₃N₄O₄PS⁻

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 128.1
  • −1 ≤ LogP ≤ 5 0.17
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 397.3
  • LogP ≤ 5 0.17
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 128.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(sc[n+]1Cc2cnc(nc2N)C(F)(F)F)CCOP(=O)([O-])[O-]
InChI 
InChI=1S/C12H14F3N4O4PS/c1-7-9(2-3-23-24(20,21)22)25-6-19(7)5-8-4-17-11(12(13,14)15)18-10(8)16/h4,6H,2-3,5H2,1H3,(H3-,16,17,18,20,21,22)/p-1
InChIKey 
ZIBIECXVPMYJCV-UHFFFAOYSA-M

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)