Ligand profile

CHEMBL605227

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_2442 — spermidine synthase

Via homolog UniProt P19623 Formula C₂₁H₃₈N₈O₃S
pchembl 7.70 ~20.0 nM
Mol. weight 482.66 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL605227
UniProt (similar protein)
P19623
pchembl
7.700 (~20.0 nM)
Target protein
VK055_2442

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 482.66 Da
LogP (Crippen) -0.02
H-bond donors 6
H-bond acceptors 12
TPSA 183.38 Ų
Rotatable bonds 15
Aromatic rings 2 / 3
Heavy atoms 33
Fraction sp³ C 0.76
Formula C₂₁H₃₈N₈O₃S

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 -0.02
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 482.7
  • LogP ≤ 5 -0.02
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 15
  • TPSA ≤ 140 Ų 183.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
NCCCNCCCCCC(CCN)SC[C@H]1OC(n2cnc3c(N)ncnc32)[C@H](O)[C@@H]1O
InChI 
InChI=1S/C21H38N8O3S/c22-7-4-10-25-9-3-1-2-5-14(6-8-23)33-11-15-17(30)18(31)21(32-15)29-13-28-16-19(24)26-12-27-20(16)29/h12-15,17-18,21,25,30-31H,1-11,22-23H2,(H2,24,26,27)/t14?,15-,17-,18-,21?/m1/s1
InChIKey 
IYEWZPHRHXRMCW-RXHHNXKZSA-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)