Ligand profile

SNW

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

Bound to: VK055_0586 — bacterial extracellular solute-binding, 3 familyprotein

Via homolog PDB 5lom UniProt Q7D447 Formula C₁₁H₂₀N₂O₈
Mol. weight 308.29 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SNW
PDB
5lom
UniProt (similar protein)
Q7D447
Target protein
VK055_0586

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 308.29 Da
LogP (Crippen) -3.90
H-bond donors 7
H-bond acceptors 8
TPSA 182.57 Ų
Rotatable bonds 7
Aromatic rings 0 / 1
Heavy atoms 21
Fraction sp³ C 0.82
Formula C₁₁H₂₀N₂O₈

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 182.6
  • −1 ≤ LogP ≤ 5 -3.90
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 308.3
  • LogP ≤ 5 -3.90
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 182.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@H]([C@H]([C@@H]([C@](O1)(CN[C@@H](CCC(=O)N)C(=O)O)O)O)O)O
InChI 
InChI=1S/C11H20N2O8/c12-7(15)2-1-5(10(18)19)13-4-11(20)9(17)8(16)6(14)3-21-11/h5-6,8-9,13-14,16-17,20H,1-4H2,(H2,12,15)(H,18,19)/t5-,6+,8+,9-,11+/m0/s1
InChIKey 
SNIATPDKUZZXAT-VISRLPHGSA-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
PF00497

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_0586.

PDB 1

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

Ligand PDB entry

ZINC 48

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

Compound Similarity (Tanimoto)