Ligand profile

DNT

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

Bound to: KP13_31481 — Fumarate reductase flavoprotein subunit

Via homolog PDB 1nen UniProt P0AC41 Formula C₁₃H₁₈N₂O₅
Mol. weight 282.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DNT
PDB
1nen
UniProt (similar protein)
P0AC41
Target protein
KP13_31481

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 282.30 Da
LogP (Crippen) 3.89
H-bond donors 1
H-bond acceptors 5
TPSA 106.51 Ų
Rotatable bonds 7
Aromatic rings 1 / 1
Heavy atoms 20
Fraction sp³ C 0.54
Formula C₁₃H₁₈N₂O₅

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 106.5
  • −1 ≤ LogP ≤ 5 3.89
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 282.3
  • LogP ≤ 5 3.89
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 106.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCC(C)c1cc(cc(c1O)[N+](=O)[O-])[N+](=O)[O-]
InChI 
InChI=1S/C13H18N2O5/c1-3-4-5-6-9(2)11-7-10(14(17)18)8-12(13(11)16)15(19)20/h7-9,16H,3-6H2,1-2H3
InChIKey 
RROCMCBQTUYDSD-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
PF01127' 'PF13534

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_31481.

PDB 35

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)