Ligand profile

JD2

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

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

Via homolog PDB 6qqy UniProt B1MDI3 Formula C₁₈H₁₄N₆
Mol. weight 314.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JD2
PDB
6qqy
UniProt (similar protein)
B1MDI3
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 314.35 Da
LogP (Crippen) 2.93
H-bond donors 2
H-bond acceptors 5
TPSA 96.31 Ų
Rotatable bonds 3
Aromatic rings 4 / 4
Heavy atoms 24
Fraction sp³ C 0.06
Formula C₁₈H₁₄N₆

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

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 96.3
  • −1 ≤ LogP ≤ 5 2.93
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 314.4
  • LogP ≤ 5 2.93
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 96.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccnc(c1)Cn2ccc3c2cc(cc3)c4c(c([nH]n4)N)C#N
InChI 
InChI=1S/C18H14N6/c19-10-15-17(22-23-18(15)20)13-5-4-12-6-8-24(16(12)9-13)11-14-3-1-2-7-21-14/h1-9H,11H2,(H3,20,22,23)
InChIKey 
OGAVRMBWGWENPE-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)