Ligand profile

ICP

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

Bound to: VK055_3099 — thiamine-phosphate pyrophosphorylase

Via homolog PDB 1g67 UniProt P39594 Formula C₆H₇N₃
Mol. weight 121.14 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ICP
PDB
1g67
UniProt (similar protein)
P39594
Target protein
VK055_3099

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 121.14 Da
LogP (Crippen) 1.02
H-bond donors 1
H-bond acceptors 2
TPSA 48.57 Ų
Rotatable bonds 0
Aromatic rings 0 / 1
Heavy atoms 9
Fraction sp³ C 0.17
Formula C₆H₇N₃

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 48.6
  • −1 ≤ LogP ≤ 5 1.02
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 121.1
  • LogP ≤ 5 1.02
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 48.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1=NC(=N)C(=C)C=N1
InChI 
InChI=1S/C6H7N3/c1-4-3-8-5(2)9-6(4)7/h3,7H,1H2,2H3
InChIKey 
AXFPKNUSOMMYRV-UHFFFAOYSA-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
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)