Ligand profile

8N9

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

Bound to: KP13_32378 — transketolase 2

Via homolog PDB 5xu9 UniProt P34736 Formula C₁₄H₂₂N₄O₉P₂S
Mol. weight 484.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
8N9
PDB
5xu9
UniProt (similar protein)
P34736
Target protein
KP13_32378

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 484.36 Da
LogP (Crippen) 1.48
H-bond donors 6
H-bond acceptors 11
TPSA 208.79 Ų
Rotatable bonds 9
Aromatic rings 1 / 2
Heavy atoms 30
Fraction sp³ C 0.43
Formula C₁₄H₂₂N₄O₉P₂S

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 208.8
  • −1 ≤ LogP ≤ 5 1.48
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 484.4
  • LogP ≤ 5 1.48
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 208.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ncc(c(n1)N)CN\2C(=C(S/C2=C(\CO)/O)CCOP(=O)(O)OP(=O)(O)O)C
InChI 
InChI=1S/C14H22N4O9P2S/c1-8-12(3-4-26-29(24,25)27-28(21,22)23)30-14(11(20)7-19)18(8)6-10-5-16-9(2)17-13(10)15/h5,19-20H,3-4,6-7H2,1-2H3,(H,24,25)(H2,15,16,17)(H2,21,22,23)/b14-11+
InChIKey 
LXZUEFPJZTWGEL-SDNWHVSQSA-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)