Ligand profile

IRN

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

Bound to: VK055_3098 — thiamine biosynthesis protein ThiC

Via homolog PDB 4s25 UniProt O82392 Formula C₈H₁₃N₂O₇P
Mol. weight 280.17 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
IRN
PDB
4s25
UniProt (similar protein)
O82392
Target protein
VK055_3098

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 280.17 Da
LogP (Crippen) -1.39
H-bond donors 4
H-bond acceptors 7
TPSA 134.27 Ų
Rotatable bonds 4
Aromatic rings 1 / 2
Heavy atoms 18
Fraction sp³ C 0.62
Formula C₈H₁₃N₂O₇P

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 134.3
  • −1 ≤ LogP ≤ 5 -1.39
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 280.2
  • LogP ≤ 5 -1.39
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 134.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cn(cn1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
InChI 
InChI=1S/C8H13N2O7P/c11-6-5(3-16-18(13,14)15)17-8(7(6)12)10-2-1-9-4-10/h1-2,4-8,11-12H,3H2,(H2,13,14,15)/t5-,6-,7-,8-/m1/s1
InChIKey 
YEBULYOZZUNFGU-WCTZXXKLSA-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
PF01964

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_3098.

PDB 2

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)