Ligand profile

482

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

Bound to: VK055_0030 — bacterial regulatory, luxR family protein

Via homolog PDB 4y15 UniProt Q8XBD0 Formula C₁₀H₁₅NO₄
Mol. weight 213.23 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
482
PDB
4y15
UniProt (similar protein)
Q8XBD0
Target protein
VK055_0030

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 213.23 Da
LogP (Crippen) 0.18
H-bond donors 1
H-bond acceptors 4
TPSA 72.47 Ų
Rotatable bonds 5
Aromatic rings 0 / 1
Heavy atoms 15
Fraction sp³ C 0.70
Formula C₁₀H₁₅NO₄

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 72.5
  • −1 ≤ LogP ≤ 5 0.18
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 213.2
  • LogP ≤ 5 0.18
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 72.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCC(=O)CC(=O)N[C@H]1CCOC1=O
InChI 
InChI=1S/C10H15NO4/c1-2-3-7(12)6-9(13)11-8-4-5-15-10(8)14/h8H,2-6H2,1H3,(H,11,13)/t8-/m0/s1
InChIKey 
YRYOXRMDHALAFL-QMMMGPOBSA-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
PF03472

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_0030.

PDB 4

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

Ligand PDB entry

ChEMBL 39

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)