Ligand profile

5OB

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

Bound to: KP13_02423 — tRNA (guanine-N(1)-)-methyltransferase

Via homolog PDB 6qo6 UniProt B1MDI3 Formula C₈H₈N₂O
Mol. weight 148.16 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
5OB
PDB
6qo6
UniProt (similar protein)
B1MDI3
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 148.16 Da
LogP (Crippen) 1.57
H-bond donors 1
H-bond acceptors 2
TPSA 37.91 Ų
Rotatable bonds 1
Aromatic rings 2 / 2
Heavy atoms 11
Fraction sp³ C 0.12
Formula C₈H₈N₂O

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 37.9
  • −1 ≤ LogP ≤ 5 1.57
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 148.2
  • LogP ≤ 5 1.57
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 37.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccc2c(c1)[nH]cn2
InChI 
InChI=1S/C8H8N2O/c1-11-6-2-3-7-8(4-6)10-5-9-7/h2-5H,1H3,(H,9,10)
InChIKey 
ILMHAGCURJPNRZ-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
PF01746

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_02423.

PDB 88

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

Ligand PDB entry

ChEMBL 38

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)