Ligand profile

5NU

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

Bound to: KP13_00801 — Uracil-DNA glycosylase

Via homolog PDB 4ws4 UniProt P9WFQ9 Formula C₄H₃N₃O₄
Mol. weight 157.08 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5NU
PDB
4ws4
UniProt (similar protein)
P9WFQ9
Target protein
KP13_00801

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 157.08 Da
LogP (Crippen) -1.03
H-bond donors 2
H-bond acceptors 4
TPSA 108.86 Ų
Rotatable bonds 1
Aromatic rings 1 / 1
Heavy atoms 11
Fraction sp³ C 0.00
Formula C₄H₃N₃O₄

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 108.9
  • −1 ≤ LogP ≤ 5 -1.03
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 157.1
  • LogP ≤ 5 -1.03
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 108.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1=C(C(=O)NC(=O)N1)[N+](=O)[O-]
InChI 
InChI=1S/C4H3N3O4/c8-3-2(7(10)11)1-5-4(9)6-3/h1H,(H2,5,6,8,9)
InChIKey 
TUARVSWVPPVUGS-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 KP13_00801.

PDB 15

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

Ligand PDB entry

ChEMBL 1

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)