Ligand profile

8EL

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

Bound to: KP13_32378 — transketolase 2

Via homolog PDB 5xsa UniProt P34736 Formula C₁₂H₂₀N₄O₇P₂S
Mol. weight 426.33 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
8EL
PDB
5xsa
UniProt (similar protein)
P34736
Target protein
KP13_32378

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 426.33 Da
LogP (Crippen) 1.72
H-bond donors 4
H-bond acceptors 9
TPSA 168.33 Ų
Rotatable bonds 8
Aromatic rings 1 / 2
Heavy atoms 26
Fraction sp³ C 0.50
Formula C₁₂H₂₀N₄O₇P₂S

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 168.3
  • −1 ≤ LogP ≤ 5 1.72
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 426.3
  • LogP ≤ 5 1.72
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 168.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ncc(c(n1)N)CN2CSC(=C2C)CCOP(=O)(O)OP(=O)(O)O
InChI 
InChI=1S/C12H20N4O7P2S/c1-8-11(3-4-22-25(20,21)23-24(17,18)19)26-7-16(8)6-10-5-14-9(2)15-12(10)13/h5H,3-4,6-7H2,1-2H3,(H,20,21)(H2,13,14,15)(H2,17,18,19)
InChIKey 
FCUXBJDJFWOWMD-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
PF00456' 'PF02779

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_32378.

PDB 23

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)