Ligand profile

Y1

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

Bound to: KP13_04222 — ATP-dependent Clp protease ATP-binding subunit clpA

Via homolog PDB 1r6o UniProt P0ABH9 Formula Y²⁺
Mol. weight 88.91 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
Y1
PDB
1r6o
UniProt (similar protein)
P0ABH9
Target protein
KP13_04222

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 88.91 Da
LogP (Crippen) -0.00
H-bond donors 0
H-bond acceptors 0
TPSA 0.00 Ų
Rotatable bonds 0
Aromatic rings 0 / 0
Heavy atoms 1
Fraction sp³ C 0.00
Formula Y²⁺

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 0.0
  • −1 ≤ LogP ≤ 5 -0.00
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 88.9
  • LogP ≤ 5 -0.00
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 0
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 0.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[Y+2]
InChI 
InChI=1S/Y/q+2
InChIKey 
KAJPZYFHSCFBCI-UHFFFAOYSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF02617

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_04222.

PDB 6

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)