Ligand profile

JCE

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

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

Via homolog PDB 6qqx UniProt B1MDI3 Formula C₁₇H₁₅N₅
Mol. weight 289.34 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JCE
PDB
6qqx
UniProt (similar protein)
B1MDI3
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 289.34 Da
LogP (Crippen) 3.06
H-bond donors 2
H-bond acceptors 4
TPSA 72.52 Ų
Rotatable bonds 3
Aromatic rings 4 / 4
Heavy atoms 22
Fraction sp³ C 0.06
Formula C₁₇H₁₅N₅

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 72.5
  • −1 ≤ LogP ≤ 5 3.06
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 289.3
  • LogP ≤ 5 3.06
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 72.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccnc(c1)Cn2ccc3c2cc(cc3)c4cc(n[nH]4)N
InChI 
InChI=1S/C17H15N5/c18-17-10-15(20-21-17)13-5-4-12-6-8-22(16(12)9-13)11-14-3-1-2-7-19-14/h1-10H,11H2,(H3,18,20,21)
InChIKey 
QCOOOKJAGFXTOZ-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)