Ligand profile

CHEMBL330673

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_2442 — spermidine synthase

Via homolog UniProt P19623 Formula C₁₈H₃₁N₇O₃S
pchembl 6.60 ~251.2 nM
Mol. weight 425.56 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL330673
UniProt (similar protein)
P19623
pchembl
6.600 (~251.2 nM)
Target protein
VK055_2442

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 425.56 Da
LogP (Crippen) -0.00
H-bond donors 5
H-bond acceptors 11
TPSA 171.35 Ų
Rotatable bonds 11
Aromatic rings 2 / 3
Heavy atoms 29
Fraction sp³ C 0.72
Formula C₁₈H₃₁N₇O₃S

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 171.3
  • −1 ≤ LogP ≤ 5 -0.00
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 425.6
  • LogP ≤ 5 -0.00
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 171.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
NCCCCCC(CCN)SC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]1O
InChI 
InChI=1S/C18H31N7O3S/c19-6-3-1-2-4-11(5-7-20)29-8-12-14(26)15(27)18(28-12)25-10-24-13-16(21)22-9-23-17(13)25/h9-12,14-15,18,26-27H,1-8,19-20H2,(H2,21,22,23)/t11?,12-,14-,15-,18-/m1/s1
InChIKey 
YETXSQDQSWLLJR-JJPFLPBXSA-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)