Ligand profile

DSH

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

Bound to: VK055_2442 — spermidine synthase

Via homolog PDB 3rw9 UniProt P19623 Formula C₁₃H₂₀N₆O₃S
Mol. weight 340.41 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DSH
PDB
3rw9
UniProt (similar protein)
P19623
Target protein
VK055_2442

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 340.41 Da
LogP (Crippen) -0.89
H-bond donors 4
H-bond acceptors 10
TPSA 145.33 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 23
Fraction sp³ C 0.62
Formula C₁₃H₂₀N₆O₃S

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 145.3
  • −1 ≤ LogP ≤ 5 -0.89
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 340.4
  • LogP ≤ 5 -0.89
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 145.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCCCN)O)O)N
InChI 
InChI=1S/C13H20N6O3S/c14-2-1-3-23-4-7-9(20)10(21)13(22-7)19-6-18-8-11(15)16-5-17-12(8)19/h5-7,9-10,13,20-21H,1-4,14H2,(H2,15,16,17)/t7-,9-,10-,13-/m1/s1
InChIKey 
FUSRAALGPJJIRO-QYVSTXNMSA-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)