Ligand profile

URA

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

Bound to: KP13_03816 — Uracil permease

Via homolog PDB 5xls UniProt P0AGM8 Formula C₄H₄N₂O₂
Mol. weight 112.09 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
URA
PDB
5xls
UniProt (similar protein)
P0AGM8
Target protein
KP13_03816

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 112.09 Da
LogP (Crippen) -0.94
H-bond donors 2
H-bond acceptors 2
TPSA 65.72 Ų
Rotatable bonds 0
Aromatic rings 1 / 1
Heavy atoms 8
Fraction sp³ C 0.00
Formula C₄H₄N₂O₂

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 65.7
  • −1 ≤ LogP ≤ 5 -0.94
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 112.1
  • LogP ≤ 5 -0.94
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 65.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1=CNC(=O)NC1=O
InChI 
InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8)
InChIKey 
ISAKRJDGNUQOIC-UHFFFAOYSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF00860

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_03816.

PDB 3

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)