Binder profile

SPD

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

Bound to: PA0295 — polyamine binding protein

Via homolog PDB 1pot UniProt P0AFK9 C7H19N3
Mol. weight 145.25 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SPD
PDB
1pot
UniProt (similar protein)
P0AFK9
Target protein
PA0295

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 145.25 Da
LogP (Crippen) -0.34
H-bond donors 3
H-bond acceptors 3
TPSA 64.07 Ų
Rotatable bonds 7
Aromatic rings 0 / 0
Heavy atoms 10
Fraction sp³ C 1.00
Formula C7H19N3

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 145.2
  • LogP ≤ 5 -0.34
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 64.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CCNCCCN)CN
InChI 
InChI=1S/C7H19N3/c8-4-1-2-6-10-7-3-5-9/h10H,1-9H2
InChIKey 
ATHGHQPFGPMSJY-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
PF13416

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 11

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)