Ligand profile

3SO

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

Bound to: VK055_0686 — L-2,4-diaminobutyrate decarboxylase

Via homolog PDB 4obv UniProt A7B1V0 Formula C₁₉H₁₉N₂O₆P
Mol. weight 402.34 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3SO
PDB
4obv
UniProt (similar protein)
A7B1V0
Target protein
VK055_0686

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 402.34 Da
LogP (Crippen) 3.01
H-bond donors 4
H-bond acceptors 5
TPSA 132.74 Ų
Rotatable bonds 7
Aromatic rings 3 / 3
Heavy atoms 28
Fraction sp³ C 0.16
Formula C₁₉H₁₉N₂O₆P

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 132.7
  • −1 ≤ LogP ≤ 5 3.01
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 402.3
  • LogP ≤ 5 3.01
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 132.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(c(cn1)COP(=O)(O)O)/C=C/C(=O)Cc2c[nH]c3c2cccc3)O
InChI 
InChI=1S/C19H19N2O6P/c1-12-19(23)17(14(10-20-12)11-27-28(24,25)26)7-6-15(22)8-13-9-21-18-5-3-2-4-16(13)18/h2-7,9-10,21,23H,8,11H2,1H3,(H2,24,25,26)/b7-6+
InChIKey 
UHCJSBYGRGJECF-VOTSOKGWSA-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
PF00282

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_0686.

PDB 4

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

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)