Ligand profile

EBM

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

Bound to: KP13_03278 — Succinate dehydrogenase iron-sulfur subunit

Via homolog PDB 3aec UniProt Q007T0 Formula C₁₀H₁₂INO
Mol. weight 289.12 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
EBM
PDB
3aec
UniProt (similar protein)
Q007T0
Target protein
KP13_03278

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 289.12 Da
LogP (Crippen) 2.43
H-bond donors 1
H-bond acceptors 1
TPSA 29.10 Ų
Rotatable bonds 2
Aromatic rings 1 / 1
Heavy atoms 13
Fraction sp³ C 0.30
Formula C₁₀H₁₂INO

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 2.43
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 289.1
  • LogP ≤ 5 2.43
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 1
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 29.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)NC(=O)c1ccccc1I
InChI 
InChI=1S/C10H12INO/c1-7(2)12-10(13)8-5-3-4-6-9(8)11/h3-7H,1-2H3,(H,12,13)
InChIKey 
PSGIDUPRPSJZRV-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' '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)