Ligand profile

SDS

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

Bound to: VK055_1877 — antimicrobial peptide resistance and lipid A acylation PagP family protein

Via homolog PDB 3gp6 UniProt P37001 Formula C₁₂H₂₆O₄S
Mol. weight 266.40 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SDS
PDB
3gp6
UniProt (similar protein)
P37001
Target protein
VK055_1877

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 266.40 Da
LogP (Crippen) 3.73
H-bond donors 1
H-bond acceptors 3
TPSA 63.60 Ų
Rotatable bonds 12
Aromatic rings 0 / 0
Heavy atoms 17
Fraction sp³ C 1.00
Formula C₁₂H₂₆O₄S

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 63.6
  • −1 ≤ LogP ≤ 5 3.73
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 266.4
  • LogP ≤ 5 3.73
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 63.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCOS(=O)(=O)O
InChI 
InChI=1S/C12H26O4S/c1-2-3-4-5-6-7-8-9-10-11-12-16-17(13,14)15/h2-12H2,1H3,(H,13,14,15)
InChIKey 
MOTZDAYCYVMXPC-UHFFFAOYSA-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
PF07017

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_1877.

PDB 1

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)