Binder profile

ZINC13377742

Virtual-screening candidate from ZINC.

Bound to: PA0295 — polyamine binding protein

Via homolog UniProt Q9I6J0 C12H30N4
Tanimoto 0.93
Mol. weight 230.40 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC13377742
UniProt (similar protein)
Q9I6J0
Tanimoto
0.929
Target protein
PA0295

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 230.40 Da
LogP (Crippen) 0.42
H-bond donors 4
H-bond acceptors 4
TPSA 76.10 Ų
Rotatable bonds 13
Aromatic rings 0 / 0
Heavy atoms 16
Fraction sp³ C 1.00
Formula C12H30N4

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 230.4
  • LogP ≤ 5 0.42
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • TPSA ≤ 140 Ų 76.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
NCCCCNCCCCNCCCCN
InChI 
InChI=1S/C12H30N4/c13-7-1-3-9-15-11-5-6-12-16-10-4-2-8-14/h15-16H,1-14H2
InChIKey 
RPSHOHKFHRFBAZ-UHFFFAOYSA-N

Provenance

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

Method
LigQ nearest_k
Query
SPD
Homolog
Q9I6J0

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA0295.

PDB 12

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)