Ligand profile

GOP

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

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

Via homolog PDB 5l9o UniProt Q7D447 Formula C₁₁H₂₂N₂O₈
Mol. weight 310.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GOP
PDB
5l9o
UniProt (similar protein)
Q7D447
Target protein
VK055_0586

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 310.30 Da
LogP (Crippen) -4.27
H-bond donors 8
H-bond acceptors 8
TPSA 193.57 Ų
Rotatable bonds 11
Aromatic rings 0 / 0
Heavy atoms 21
Fraction sp³ C 0.82
Formula C₁₁H₂₂N₂O₈

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 193.6
  • −1 ≤ LogP ≤ 5 -4.27
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 310.3
  • LogP ≤ 5 -4.27
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 193.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CC(=O)N)[C@@H](C(=O)O)NC[C@@H]([C@H]([C@@H]([C@@H](CO)O)O)O)O
InChI 
InChI=1S/C11H22N2O8/c12-8(17)2-1-5(11(20)21)13-3-6(15)9(18)10(19)7(16)4-14/h5-7,9-10,13-16,18-19H,1-4H2,(H2,12,17)(H,20,21)/t5-,6-,7+,9+,10+/m0/s1
InChIKey 
VPRLICVDSGMIKO-ZSAGQLGGSA-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)