Ligand profile

JDQ

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

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

Via homolog PDB 6qqw UniProt B1MDI3 Formula C₁₈H₁₆N₄
Mol. weight 288.35 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JDQ
PDB
6qqw
UniProt (similar protein)
B1MDI3
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 288.35 Da
LogP (Crippen) 3.66
H-bond donors 2
H-bond acceptors 3
TPSA 59.63 Ų
Rotatable bonds 3
Aromatic rings 4 / 4
Heavy atoms 22
Fraction sp³ C 0.06
Formula C₁₈H₁₆N₄

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 59.6
  • −1 ≤ LogP ≤ 5 3.66
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 288.4
  • LogP ≤ 5 3.66
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 59.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)Cn2ccc3c2cc(cc3)c4cc([nH]n4)N
InChI 
InChI=1S/C18H16N4/c19-18-11-16(20-21-18)15-7-6-14-8-9-22(17(14)10-15)12-13-4-2-1-3-5-13/h1-11H,12H2,(H3,19,20,21)
InChIKey 
IXGUTMYAJBKSPV-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)