Ligand profile

O3Y

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

Bound to: KP13_00363 — LpxA-like domain-containing transferase

Via homolog PDB 6p83 UniProt P21645 Formula C₂₄H₂₀ClN₃O₂
Mol. weight 417.90 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
O3Y
PDB
6p83
UniProt (similar protein)
P21645
Target protein
KP13_00363

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 417.90 Da
LogP (Crippen) 5.60
H-bond donors 1
H-bond acceptors 5
TPSA 68.01 Ų
Rotatable bonds 2
Aromatic rings 4 / 5
Heavy atoms 30
Fraction sp³ C 0.21
Formula C₂₄H₂₀ClN₃O₂

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 68.0
  • −1 ≤ LogP ≤ 5 5.60
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 417.9
  • LogP ≤ 5 5.60
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 68.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1(Cc2c(c(c3c(n2)nn(c3O)c4ccccc4)c5ccccc5Cl)C(=O)C1)C
InChI 
InChI=1S/C24H20ClN3O2/c1-24(2)12-17-20(18(29)13-24)19(15-10-6-7-11-16(15)25)21-22(26-17)27-28(23(21)30)14-8-4-3-5-9-14/h3-11,30H,12-13H2,1-2H3
InChIKey 
RZRIAROHONSNNR-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
PF00132' 'PF04613

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_00363.

PDB 15

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)