Ligand profile

JCK

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

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

Via homolog PDB 6qr6 UniProt B1MDI3 Formula C₂₄H₂₄N₆
Mol. weight 396.50 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JCK
PDB
6qr6
UniProt (similar protein)
B1MDI3
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 396.50 Da
LogP (Crippen) 4.13
H-bond donors 2
H-bond acceptors 5
TPSA 86.66 Ų
Rotatable bonds 5
Aromatic rings 4 / 5
Heavy atoms 30
Fraction sp³ C 0.25
Formula C₂₄H₂₄N₆

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 86.7
  • −1 ≤ LogP ≤ 5 4.13
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 396.5
  • LogP ≤ 5 4.13
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 86.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1Cn2ccc3c2cc(cc3)c4c(c([nH]n4)N)C#N)CN5CCCC5
InChI 
InChI=1S/C24H24N6/c25-14-21-23(27-28-24(21)26)20-8-7-19-9-12-30(22(19)13-20)16-18-5-3-17(4-6-18)15-29-10-1-2-11-29/h3-9,12-13H,1-2,10-11,15-16H2,(H3,26,27,28)
InChIKey 
IWWBYCSSMDZNIG-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)