Ligand profile

3EE

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

Bound to: VK055_0552 — fused predicted DNA-binding transcriptional regulator and predicted amino transferase

Via homolog PDB 3wx9 UniProt O57946 Formula C₁₀H₉NO₄
Mol. weight 207.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3EE
PDB
3wx9
UniProt (similar protein)
O57946
Target protein
VK055_0552

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 207.18 Da
LogP (Crippen) 0.50
H-bond donors 2
H-bond acceptors 4
TPSA 97.46 Ų
Rotatable bonds 4
Aromatic rings 1 / 1
Heavy atoms 15
Fraction sp³ C 0.10
Formula C₁₀H₉NO₄

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 97.5
  • −1 ≤ LogP ≤ 5 0.50
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 207.2
  • LogP ≤ 5 0.50
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 97.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(c(c1)C(=O)CC(=O)C(=O)O)N
InChI 
InChI=1S/C10H9NO4/c11-7-4-2-1-3-6(7)8(12)5-9(13)10(14)15/h1-4H,5,11H2,(H,14,15)
InChIKey 
CAOVWYZQMPNAFJ-UHFFFAOYSA-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
PF00155

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_0552.

PDB 19

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

Ligand PDB entry

ChEMBL 100

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)