Ligand profile

PUT

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

Bound to: VK055_2442 — spermidine synthase

Via homolog PDB 2o06 UniProt P19623 Formula C₄H₁₂N₂
Mol. weight 88.15 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PUT
PDB
2o06
UniProt (similar protein)
P19623
Target protein
VK055_2442

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 88.15 Da
LogP (Crippen) -0.32
H-bond donors 2
H-bond acceptors 2
TPSA 52.04 Ų
Rotatable bonds 3
Aromatic rings 0 / 0
Heavy atoms 6
Fraction sp³ C 1.00
Formula C₄H₁₂N₂

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 52.0
  • −1 ≤ LogP ≤ 5 -0.32
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 88.2
  • LogP ≤ 5 -0.32
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 52.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CCN)CN
InChI 
InChI=1S/C4H12N2/c5-3-1-2-4-6/h1-6H2
InChIKey 
KIDHWZJUCRJVML-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
PF01564' 'PF17284

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to VK055_2442.

PDB 7

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

Ligand PDB entry

ChEMBL 4

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)