Ligand profile

HSO

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

Bound to: KP13_00862 — Histidyl-tRNA synthetase

Via homolog PDB 1kmn UniProt P60906 Formula C₆H₁₂N₃O⁺
Mol. weight 142.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HSO
PDB
1kmn
UniProt (similar protein)
P60906
Target protein
KP13_00862

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 142.18 Da
LogP (Crippen) -1.31
H-bond donors 3
H-bond acceptors 2
TPSA 76.18 Ų
Rotatable bonds 3
Aromatic rings 1 / 1
Heavy atoms 10
Fraction sp³ C 0.50
Formula C₆H₁₂N₃O⁺

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 76.2
  • −1 ≤ LogP ≤ 5 -1.31
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 142.2
  • LogP ≤ 5 -1.31
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 76.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c([nH+]c[nH]1)C[C@@H](CO)N
InChI 
InChI=1S/C6H11N3O/c7-5(3-10)1-6-2-8-4-9-6/h2,4-5,10H,1,3,7H2,(H,8,9)/p+1/t5-/m0/s1
InChIKey 
ZQISRDCJNBUVMM-YFKPBYRVSA-O

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
PF00587

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_00862.

PDB 2

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)