Ligand profile

ZINC1727446

Virtual-screening candidate from ZINC.

Bound to: VK055_3994 — uracil DNA glycosylase superfamily protein

Via homolog UniProt Q13569 Formula C₉H₁₂N₄O₅
Tanimoto 0.54
Mol. weight 256.22 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC1727446
UniProt (similar protein)
Q13569
Tanimoto
0.537
Target protein
VK055_3994

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 256.22 Da
LogP (Crippen) -2.08
H-bond donors 5
H-bond acceptors 6
TPSA 158.40 Ų
Rotatable bonds 4
Aromatic rings 1 / 1
Heavy atoms 18
Fraction sp³ C 0.33
Formula C₉H₁₂N₄O₅

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 158.4
  • −1 ≤ LogP ≤ 5 -2.08
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 256.2
  • LogP ≤ 5 -2.08
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 158.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H](O)[C@H](NC(=O)c1c[nH]c(=O)nc1N)C(=O)O
InChI 
InChI=1S/C9H12N4O5/c1-3(14)5(8(16)17)12-7(15)4-2-11-9(18)13-6(4)10/h2-3,5,14H,1H3,(H,12,15)(H,16,17)(H3,10,11,13,18)/t3-,5+/m1/s1
InChIKey 
AMGXTZHMKHVLFM-WUJLRWPWSA-N

Provenance

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

Method
LigQ nearest_k
Query
1RT
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)