Ligand profile

SPM

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

Bound to: KP13_05529 — N-Acetyltransferase domain-containing protein

Via homolog PDB 4mi4 UniProt Q9KL03 Formula C₁₀H₂₆N₄
Mol. weight 202.35 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SPM
PDB
4mi4
UniProt (similar protein)
Q9KL03
Target protein
KP13_05529

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.

  • TPSA ≤ 90 Ų 76.1
  • −1 ≤ LogP ≤ 5 -0.36
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 Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00583

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_05529.

PDB 7

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)