Ligand profile

CHEMBL608868

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_2442 — spermidine synthase

Via homolog UniProt P19623 Formula C₁₈H₃₂N₈O₃
pchembl 8.52 ~3.0 nM
Mol. weight 408.51 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL608868
UniProt (similar protein)
P19623
pchembl
8.520 (~3.0 nM)
Target protein
VK055_2442

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 408.51 Da
LogP (Crippen) -1.15
H-bond donors 6
H-bond acceptors 11
TPSA 183.38 Ų
Rotatable bonds 11
Aromatic rings 2 / 3
Heavy atoms 29
Fraction sp³ C 0.72
Formula C₁₈H₃₂N₈O₃

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

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 183.4
  • −1 ≤ LogP ≤ 5 -1.15
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 408.5
  • LogP ≤ 5 -1.15
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 183.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
NCCCCNC(CCN)CC[C@H]1OC(n2cnc3c(N)ncnc32)[C@H](O)[C@@H]1O
InChI 
InChI=1S/C18H32N8O3/c19-6-1-2-8-22-11(5-7-20)3-4-12-14(27)15(28)18(29-12)26-10-25-13-16(21)23-9-24-17(13)26/h9-12,14-15,18,22,27-28H,1-8,19-20H2,(H2,21,23,24)/t11?,12-,14-,15-,18?/m1/s1
InChIKey 
QWWYIMOIEWLIOP-WFIMNSBASA-N

Provenance

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

Method
LigQ nearest_k
Source
ChEMBL
Curation
pdb_similarity_tanimoto
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 8

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

Ligand PDB entry

ChEMBL 3

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)