Ligand profile

ZINC1682039

Virtual-screening candidate from ZINC.

Bound to: VK055_3994 — uracil DNA glycosylase superfamily protein

Via homolog UniProt Q13569 Formula C₉H₁₅N₃O₄
Tanimoto 0.59
Mol. weight 229.24 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC1682039
UniProt (similar protein)
Q13569
Tanimoto
0.594
Target protein
VK055_3994

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 229.24 Da
LogP (Crippen) -2.15
H-bond donors 4
H-bond acceptors 5
TPSA 109.42 Ų
Rotatable bonds 6
Aromatic rings 1 / 1
Heavy atoms 16
Fraction sp³ C 0.56
Formula C₉H₁₅N₃O₄

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 109.4
  • −1 ≤ LogP ≤ 5 -2.15
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 229.2
  • LogP ≤ 5 -2.15
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 109.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=c1[nH]cc(CN(CCO)CCO)c(=O)[nH]1
InChI 
InChI=1S/C9H15N3O4/c13-3-1-12(2-4-14)6-7-5-10-9(16)11-8(7)15/h5,13-14H,1-4,6H2,(H2,10,11,15,16)
InChIKey 
RYXYCGUBRDLBCL-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
HMU
Homolog
Q13569

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_3994.

PDB 2

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 13

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)