Ligand profile

O4D

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

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

Via homolog PDB 6p8a UniProt P21645 Formula C₂₁H₂₈N₆O₂
Mol. weight 396.50 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
O4D
PDB
6p8a
UniProt (similar protein)
P21645
Target protein
KP13_00363

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 396.50 Da
LogP (Crippen) 1.68
H-bond donors 1
H-bond acceptors 7
TPSA 77.21 Ų
Rotatable bonds 7
Aromatic rings 3 / 4
Heavy atoms 29
Fraction sp³ C 0.48
Formula C₂₁H₂₈N₆O₂

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 77.2
  • −1 ≤ LogP ≤ 5 1.68
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 396.5
  • LogP ≤ 5 1.68
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 77.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc(nc2c1c(nn2CC(=O)NCCCN3CCOCC3)n4cccc4)C
InChI 
InChI=1S/C21H28N6O2/c1-16-14-17(2)23-20-19(16)21(26-8-3-4-9-26)24-27(20)15-18(28)22-6-5-7-25-10-12-29-13-11-25/h3-4,8-9,14H,5-7,10-13,15H2,1-2H3,(H,22,28)
InChIKey 
AZMBNAXBTVHIKQ-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

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)