Ligand profile

B6X

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

Bound to: VK055_0143 — FAD dependent oxidoreductase family protein

Via homolog PDB 6j39 UniProt X5IYZ1 Formula C₁₁H₂₀O₄S
Mol. weight 248.34 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
B6X
PDB
6j39
UniProt (similar protein)
X5IYZ1
Target protein
VK055_0143

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 248.34 Da
LogP (Crippen) 2.62
H-bond donors 2
H-bond acceptors 3
TPSA 74.60 Ų
Rotatable bonds 10
Aromatic rings 0 / 0
Heavy atoms 16
Fraction sp³ C 0.82
Formula C₁₁H₂₀O₄S

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 74.6
  • −1 ≤ LogP ≤ 5 2.62
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 248.3
  • LogP ≤ 5 2.62
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 74.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCC[C@H](CC(=O)O)SCC(=O)O
InChI 
InChI=1S/C11H20O4S/c1-2-3-4-5-6-9(7-10(12)13)16-8-11(14)15/h9H,2-8H2,1H3,(H,12,13)(H,14,15)/t9-/m1/s1
InChIKey 
YVPPUISYPJOKND-SECBINFHSA-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
PF01266

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_0143.

PDB 8

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)