Ligand profile

EDT

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

Bound to: KP13_00845 — Cysteine desulfurase

Via homolog PDB 6uxe UniProt Q9Y697 Formula C₁₀H₁₆N₂O₈
Mol. weight 292.24 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
EDT
PDB
6uxe
UniProt (similar protein)
Q9Y697
Target protein
KP13_00845

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 292.24 Da
LogP (Crippen) -2.07
H-bond donors 4
H-bond acceptors 6
TPSA 155.68 Ų
Rotatable bonds 11
Aromatic rings 0 / 0
Heavy atoms 20
Fraction sp³ C 0.60
Formula C₁₀H₁₆N₂O₈

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 155.7
  • −1 ≤ LogP ≤ 5 -2.07
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 292.2
  • LogP ≤ 5 -2.07
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 155.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CN(CC(=O)O)CC(=O)O)N(CC(=O)O)CC(=O)O
InChI 
InChI=1S/C10H16N2O8/c13-7(14)3-11(4-8(15)16)1-2-12(5-9(17)18)6-10(19)20/h1-6H2,(H,13,14)(H,15,16)(H,17,18)(H,19,20)
InChIKey 
KCXVZYZYPLLWCC-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
PF00266' 'PF05347

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_00845.

PDB 10

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)