Ligand profile

E23

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

Bound to: KP13_03278 — Succinate dehydrogenase iron-sulfur subunit

Via homolog PDB 4ysx UniProt O44074 Formula C₁₉H₂₀F₃NO
Mol. weight 335.37 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
E23
PDB
4ysx
UniProt (similar protein)
O44074
Target protein
KP13_03278

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 335.37 Da
LogP (Crippen) 4.93
H-bond donors 1
H-bond acceptors 1
TPSA 29.10 Ų
Rotatable bonds 3
Aromatic rings 2 / 2
Heavy atoms 24
Fraction sp³ C 0.32
Formula C₁₉H₂₀F₃NO

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 29.1
  • −1 ≤ LogP ≤ 5 4.93
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 335.4
  • LogP ≤ 5 4.93
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 1
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 29.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(C)c1ccc(cc1)CNC(=O)c2ccccc2C(F)(F)F
InChI 
InChI=1S/C19H20F3NO/c1-18(2,3)14-10-8-13(9-11-14)12-23-17(24)15-6-4-5-7-16(15)19(20,21)22/h4-11H,12H2,1-3H3,(H,23,24)
InChIKey 
RYYHDFPDKHYSSE-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
PF01127' 'PF05328' 'PF13534

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_03278.

PDB 44

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)