Ligand profile

DON

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

Bound to: VK055_0721 — putative gamma-glutamyltransferase ywrD

Via homolog PDB 5y9b UniProt Q65KZ6 Formula C₆H₁₁N₃O₃
Mol. weight 173.17 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
DON
PDB
5y9b
UniProt (similar protein)
Q65KZ6
Target protein
VK055_0721

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 173.17 Da
LogP (Crippen) -0.22
H-bond donors 3
H-bond acceptors 5
TPSA 116.60 Ų
Rotatable bonds 6
Aromatic rings 0 / 0
Heavy atoms 12
Fraction sp³ C 0.67
Formula C₆H₁₁N₃O₃

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 116.6
  • −1 ≤ LogP ≤ 5 -0.22
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 173.2
  • LogP ≤ 5 -0.22
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 116.6
PAINS Alert

Matches PAINS filter: azo_A(324). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CC(=O)CN=N)[C@@H](C(=O)O)N
InChI 
InChI=1S/C6H11N3O3/c7-5(6(11)12)2-1-4(10)3-9-8/h5,8H,1-3,7H2,(H,11,12)/t5-/m0/s1
InChIKey 
CKRLZVNSTCQAJW-YFKPBYRVSA-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
PF01019

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_0721.

PDB 7

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)