Ligand profile

J9T

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

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

Via homolog PDB 6qok UniProt B1MDI3 Formula C₇H₈N₂O₂
Mol. weight 152.15 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
J9T
PDB
6qok
UniProt (similar protein)
B1MDI3
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 152.15 Da
LogP (Crippen) 0.45
H-bond donors 1
H-bond acceptors 4
TPSA 65.21 Ų
Rotatable bonds 1
Aromatic rings 1 / 1
Heavy atoms 11
Fraction sp³ C 0.14
Formula C₇H₈N₂O₂

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 65.2
  • −1 ≤ LogP ≤ 5 0.45
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 152.2
  • LogP ≤ 5 0.45
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 65.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COC(=O)c1ccnc(c1)N
InChI 
InChI=1S/C7H8N2O2/c1-11-7(10)5-2-3-9-6(8)4-5/h2-4H,1H3,(H2,8,9)
InChIKey 
SVWWNEYBEFASMP-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)