Ligand profile

46E

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

Bound to: KP13_26403 — Phosphatidylglycerophosphatase B

Via homolog PDB 5jwy UniProt P0A924 Formula C₃₃H₆₆NO₈P
Mol. weight 635.86 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
46E
PDB
5jwy
UniProt (similar protein)
P0A924
Target protein
KP13_26403

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 635.86 Da
LogP (Crippen) 8.94
H-bond donors 2
H-bond acceptors 8
TPSA 134.38 Ų
Rotatable bonds 33
Aromatic rings 0 / 0
Heavy atoms 43
Fraction sp³ C 0.94
Formula C₃₃H₆₆NO₈P

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 8.94
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 635.9
  • LogP ≤ 5 8.94
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 33
  • TPSA ≤ 140 Ų 134.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN)OC(=O)CCCCCCCCCCCCC
InChI 
InChI=1S/C33H66NO8P/c1-3-5-7-9-11-13-15-17-19-21-23-25-32(35)39-29-31(30-41-43(37,38)40-28-27-34)42-33(36)26-24-22-20-18-16-14-12-10-8-6-4-2/h31H,3-30,34H2,1-2H3,(H,37,38)/t31-/m1/s1
InChIKey 
NEZDNQCXEZDCBI-WJOKGBTCSA-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
PF01569

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_26403.

ZINC 50

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

Compound Similarity (Tanimoto)