Binder profile

BEN

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

Bound to: PA3417 — pyruvate dehydrogenase E1 component subunit alpha

Via homolog PDB 1v11 UniProt P12694 C7H8N2
Mol. weight 120.15 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
BEN
PDB
1v11
UniProt (similar protein)
P12694
Target protein
PA3417

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 120.15 Da
LogP (Crippen) 0.97
H-bond donors 2
H-bond acceptors 1
TPSA 49.87 Ų
Rotatable bonds 1
Aromatic rings 1 / 1
Heavy atoms 9
Fraction sp³ C 0.00
Formula C7H8N2

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.

Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 120.2
  • LogP ≤ 5 0.97
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 1
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 49.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[H]/N=C(\c1ccccc1)/N
InChI 
InChI=1S/C7H8N2/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H3,8,9)
InChIKey 
PXXJHWLDUBFPOL-UHFFFAOYSA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00676

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other binders for this protein

Quick navigation to other ligands bound to PA3417.

PDB 7

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)