Ligand profile

U5N

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

Bound to: VK055_0488 — pentaerythritol tetranitrate reductase

Via homolog PDB 7bn6 UniProt M2XAQ9 Formula C₅H₆O₂
Mol. weight 98.10 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
U5N
PDB
7bn6
UniProt (similar protein)
M2XAQ9
Target protein
VK055_0488

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 98.10 Da
LogP (Crippen) 0.49
H-bond donors 0
H-bond acceptors 2
TPSA 26.30 Ų
Rotatable bonds 0
Aromatic rings 0 / 1
Heavy atoms 7
Fraction sp³ C 0.40
Formula C₅H₆O₂

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 26.3
  • −1 ≤ LogP ≤ 5 0.49
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 98.1
  • LogP ≤ 5 0.49
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 26.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1C=CC(=O)O1
InChI 
InChI=1S/C5H6O2/c1-4-2-3-5(6)7-4/h2-4H,1H3/t4-/m1/s1
InChIKey 
BGLUXFNVVSVEET-SCSAIBSYSA-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
PF00724

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_0488.

PDB 19

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)