Binder profile

SPM

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

Bound to: PA0295 — polyamine binding protein

Via homolog PDB 6yec UniProt P31133 C10H26N4
Mol. weight 202.35 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SPM
PDB
6yec
UniProt (similar protein)
P31133
Target protein
PA0295

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 202.35 Da
LogP (Crippen) -0.36
H-bond donors 4
H-bond acceptors 4
TPSA 76.10 Ų
Rotatable bonds 11
Aromatic rings 0 / 0
Heavy atoms 14
Fraction sp³ C 1.00
Formula C10H26N4

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 202.3
  • LogP ≤ 5 -0.36
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 76.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CCNCCCN)CNCCCN
InChI 
InChI=1S/C10H26N4/c11-5-3-9-13-7-1-2-8-14-10-4-6-12/h13-14H,1-12H2
InChIKey 
PFNFFQXMRSDOHW-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)