Ligand profile

CHEMBL404271

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_04561 — putative glycosidase

Via homolog UniProt P94451 Formula C₂₅H₄₃NO₁₈
pchembl 6.47 ~338.8 nM
Mol. weight 645.61 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL404271
UniProt (similar protein)
P94451
pchembl
6.470 (~338.8 nM)
Target protein
KP13_04561

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 645.61 Da
LogP (Crippen) -8.56
H-bond donors 14
H-bond acceptors 19
TPSA 321.17 Ų
Rotatable bonds 9
Aromatic rings 0 / 4
Heavy atoms 44
Fraction sp³ C 0.92
Formula C₂₅H₄₃NO₁₈

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 321.2
  • −1 ≤ LogP ≤ 5 -8.56
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 645.6
  • LogP ≤ 5 -8.56
  • H-bond donors ≤ 5 14
  • H-bond acceptors ≤ 10 19
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 321.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H]1O[C@H](O[C@H]2[C@H](O)[C@@H](O)[C@@H](O[C@H]3[C@H](O)[C@@H](O)C(O)O[C@@H]3CO)O[C@@H]2CO)[C@H](O)[C@@H](O)[C@@H]1N[C@H]1C=C(CO)[C@@H](O)[C@H](O)[C@H]1O
InChI 
InChI=1S/C25H43NO18/c1-6-11(26-8-2-7(3-27)12(30)15(33)13(8)31)14(32)19(37)24(40-6)43-22-10(5-29)42-25(20(38)17(22)35)44-21-9(4-28)41-23(39)18(36)16(21)34/h2,6,8-39H,3-5H2,1H3/t6-,8+,9-,10-,11-,12-,13+,14+,15+,16-,17-,18-,19-,20-,21-,22-,23?,24-,25-/m1/s1
InChIKey 
XUFXOAAUWZOOIT-UGEKTDRHSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
ChEMBL
Curation
pdb_similarity_tanimoto
Binding sites
PF00128

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_04561.

PDB 3

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)