Ligand profile

PRU

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

Bound to: KP13_04561 — putative glycosidase

Via homolog PDB 3wy1 UniProt H3K096 Formula C₁₂H₁₈O₈
Mol. weight 290.27 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PRU
PDB
3wy1
UniProt (similar protein)
H3K096
Target protein
KP13_04561

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 290.27 Da
LogP (Crippen) 0.75
H-bond donors 4
H-bond acceptors 4
TPSA 149.20 Ų
Rotatable bonds 10
Aromatic rings 0 / 0
Heavy atoms 20
Fraction sp³ C 0.67
Formula C₁₂H₁₈O₈

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 149.2
  • −1 ≤ LogP ≤ 5 0.75
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 290.3
  • LogP ≤ 5 0.75
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Fail
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 149.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H](C[C@H](C[C@@H](CCC(=O)O)C(=O)O)C(=O)O)C(=O)O
InChI 
InChI=1S/C12H18O8/c1-6(10(15)16)4-8(12(19)20)5-7(11(17)18)2-3-9(13)14/h6-8H,2-5H2,1H3,(H,13,14)(H,15,16)(H,17,18)(H,19,20)/t6-,7-,8-/m1/s1
InChIKey 
UEYGDIASMOPQFG-BWZBUEFSSA-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
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 2

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 1

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)