Ligand profile

1RT

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

Bound to: VK055_3994 — uracil DNA glycosylase superfamily protein

Via homolog PDB 4jgc UniProt Q13569 Formula C₅H₅N₃O₃
Mol. weight 155.11 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1RT
PDB
4jgc
UniProt (similar protein)
Q13569
Target protein
VK055_3994

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 155.11 Da
LogP (Crippen) -0.95
H-bond donors 3
H-bond acceptors 4
TPSA 109.07 Ų
Rotatable bonds 1
Aromatic rings 1 / 1
Heavy atoms 11
Fraction sp³ C 0.00
Formula C₅H₅N₃O₃

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 109.1
  • −1 ≤ LogP ≤ 5 -0.95
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 155.1
  • LogP ≤ 5 -0.95
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 109.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1=C(C(=NC(=O)N1)N)C(=O)O
InChI 
InChI=1S/C5H5N3O3/c6-3-2(4(9)10)1-7-5(11)8-3/h1H,(H,9,10)(H3,6,7,8,11)
InChIKey 
BLQMCTXZEMGOJM-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
PF03167

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 1

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

Ligand PDB entry

ZINC 14

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

Compound Similarity (Tanimoto)