Ligand profile

ADE

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

Bound to: VK055_0819 — serine/threonine kinase HipA

Via homolog PDB 3tpv UniProt P23874 Formula C₅H₅N₅
Mol. weight 135.13 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ADE
PDB
3tpv
UniProt (similar protein)
P23874
Target protein
VK055_0819

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 135.13 Da
LogP (Crippen) -0.06
H-bond donors 2
H-bond acceptors 4
TPSA 80.48 Ų
Rotatable bonds 0
Aromatic rings 2 / 2
Heavy atoms 10
Fraction sp³ C 0.00
Formula C₅H₅N₅

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 80.5
  • −1 ≤ LogP ≤ 5 -0.06
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 135.1
  • LogP ≤ 5 -0.06
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 80.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1[nH]c2c(n1)c(ncn2)N
InChI 
InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10)
InChIKey 
GFFGJBXGBJISGV-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
PF07804

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_0819.

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)