Ligand profile

3PE

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

Bound to: KP13_31481 — Fumarate reductase flavoprotein subunit

Via homolog PDB 6myo UniProt Q9YHT1 Formula C₄₁H₈₂NO₈P
Mol. weight 748.08 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3PE
PDB
6myo
UniProt (similar protein)
Q9YHT1
Target protein
KP13_31481

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 748.08 Da
LogP (Crippen) 12.06
H-bond donors 2
H-bond acceptors 8
TPSA 134.38 Ų
Rotatable bonds 41
Aromatic rings 0 / 0
Heavy atoms 51
Fraction sp³ C 0.95
Formula C₄₁H₈₂NO₈P

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 134.4
  • −1 ≤ LogP ≤ 5 12.06
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 748.1
  • LogP ≤ 5 12.06
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 41
  • TPSA ≤ 140 Ų 134.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN)OC(=O)CCCCCCCCCCCCCCCCC
InChI 
InChI=1S/C41H82NO8P/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-40(43)47-37-39(38-49-51(45,46)48-36-35-42)50-41(44)34-32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h39H,3-38,42H2,1-2H3,(H,45,46)/t39-/m1/s1
InChIKey 
LVNGJLRDBYCPGB-LDLOPFEMSA-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
PF01127

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_31481.

PDB 35

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)