Ligand profile

PE3

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

Bound to: KP13_00203 — putative 8-amino-7-oxononanoate synthase/2-amino-3-ketobutyrate coenzyme A ligase

Via homolog PDB 5txt UniProt P09950 Formula C₂₈H₅₈O₁₅
Mol. weight 634.76 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PE3
PDB
5txt
UniProt (similar protein)
P09950
Target protein
KP13_00203

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 634.76 Da
LogP (Crippen) -0.81
H-bond donors 2
H-bond acceptors 15
TPSA 160.45 Ų
Rotatable bonds 40
Aromatic rings 0 / 0
Heavy atoms 43
Fraction sp³ C 1.00
Formula C₂₈H₅₈O₁₅

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 160.5
  • −1 ≤ LogP ≤ 5 -0.81
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 634.8
  • LogP ≤ 5 -0.81
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 40
  • TPSA ≤ 140 Ų 160.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO)O
InChI 
InChI=1S/C28H58O15/c29-1-3-31-5-7-33-9-11-35-13-15-37-17-19-39-21-23-41-25-27-43-28-26-42-24-22-40-20-18-38-16-14-36-12-10-34-8-6-32-4-2-30/h29-30H,1-28H2
InChIKey 
ILLKMACMBHTSHP-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 KP13_00203.

PDB 32

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

Ligand PDB entry

ChEMBL 1

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)