Ligand profile

AAT

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

Bound to: VK055_2442 — spermidine synthase

Via homolog PDB 1jq3 UniProt Q9WZC2 Formula C₁₈H₂₉N₇O₃S
Mol. weight 423.54 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
AAT
PDB
1jq3
UniProt (similar protein)
Q9WZC2
Target protein
VK055_2442

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 423.54 Da
LogP (Crippen) 0.12
H-bond donors 5
H-bond acceptors 11
TPSA 171.35 Ų
Rotatable bonds 10
Aromatic rings 2 / 3
Heavy atoms 29
Fraction sp³ C 0.61
Formula C₁₈H₂₉N₇O₃S

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 0.12
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 423.5
  • LogP ≤ 5 0.12
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 171.3
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)CSC(=CCN)CCCCCN)O)O)N
InChI 
InChI=1S/C18H29N7O3S/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/h5,9-10,12,14-15,18,26-27H,1-4,6-8,19-20H2,(H2,21,22,23)/t12-,14-,15-,18-/m1/s1
InChIKey 
SUUGLGYBZXSJAA-SCFUHWHPSA-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)