Ligand profile

P80

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

Bound to: VK055_0488 — pentaerythritol tetranitrate reductase

Via homolog PDB 3p80 UniProt P71278 Formula C₈H₇NO₃
Mol. weight 165.15 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
P80
PDB
3p80
UniProt (similar protein)
P71278
Target protein
VK055_0488

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 165.15 Da
LogP (Crippen) 1.64
H-bond donors 1
H-bond acceptors 3
TPSA 63.37 Ų
Rotatable bonds 2
Aromatic rings 1 / 1
Heavy atoms 12
Fraction sp³ C 0.00
Formula C₈H₇NO₃

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 63.4
  • −1 ≤ LogP ≤ 5 1.64
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 165.1
  • LogP ≤ 5 1.64
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 63.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(cc(c1)O)/C=C/[N+](=O)[O-]
InChI 
InChI=1S/C8H7NO3/c10-8-3-1-2-7(6-8)4-5-9(11)12/h1-6,10H/b5-4+
InChIKey 
DHTXBJQMDPODIB-SNAWJCMRSA-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)