Ligand profile

8UX

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

Bound to: VK055_0630 — bacterial extracellular solute-binding, 5 Middlefamily protein

Via homolog PDB 5yh8 UniProt Q2FVE7 Formula C₁₃H₂₀N₄O₆
Mol. weight 328.33 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
8UX
PDB
5yh8
UniProt (similar protein)
Q2FVE7
Target protein
VK055_0630

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 328.33 Da
LogP (Crippen) -1.10
H-bond donors 6
H-bond acceptors 6
TPSA 164.64 Ų
Rotatable bonds 11
Aromatic rings 1 / 1
Heavy atoms 23
Fraction sp³ C 0.54
Formula C₁₃H₂₀N₄O₆

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 164.6
  • −1 ≤ LogP ≤ 5 -1.10
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 328.3
  • LogP ≤ 5 -1.10
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 164.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H](C(=O)O)N[C@@H](CCN[C@H](Cc1c[nH]cn1)C(=O)O)C(=O)O
InChI 
InChI=1S/C13H20N4O6/c1-7(11(18)19)17-9(12(20)21)2-3-15-10(13(22)23)4-8-5-14-6-16-8/h5-7,9-10,15,17H,2-4H2,1H3,(H,14,16)(H,18,19)(H,20,21)(H,22,23)/t7-,9-,10+/m0/s1
InChIKey 
WLNNYKMTYVPSDL-UJNFCWOMSA-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
PF00496

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_0630.

PDB 16

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)