Ligand profile

JDE

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

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

Via homolog PDB 6qqq UniProt B1MDI3 Formula C₁₇H₁₅N₃O₃
Mol. weight 309.32 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JDE
PDB
6qqq
UniProt (similar protein)
B1MDI3
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 309.32 Da
LogP (Crippen) 2.84
H-bond donors 1
H-bond acceptors 5
TPSA 77.10 Ų
Rotatable bonds 5
Aromatic rings 3 / 3
Heavy atoms 23
Fraction sp³ C 0.12
Formula C₁₇H₁₅N₃O₃

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 77.1
  • −1 ≤ LogP ≤ 5 2.84
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 309.3
  • LogP ≤ 5 2.84
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 77.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1cc(cc(c1)c2cccnc2)COC(=O)c3c[nH]nc3
InChI 
InChI=1S/C17H15N3O3/c1-22-16-6-12(11-23-17(21)15-9-19-20-10-15)5-14(7-16)13-3-2-4-18-8-13/h2-10H,11H2,1H3,(H,19,20)
InChIKey 
JWEGKKOSKAIWMV-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)