Ligand profile

JDK

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

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

Via homolog PDB 6qra UniProt B1MDI3 Formula C₂₄H₂₇N₅
Mol. weight 385.52 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JDK
PDB
6qra
UniProt (similar protein)
B1MDI3
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 385.52 Da
LogP (Crippen) 4.65
H-bond donors 2
H-bond acceptors 4
TPSA 62.87 Ų
Rotatable bonds 5
Aromatic rings 4 / 5
Heavy atoms 29
Fraction sp³ C 0.29
Formula C₂₄H₂₇N₅

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 62.9
  • −1 ≤ LogP ≤ 5 4.65
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 385.5
  • LogP ≤ 5 4.65
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 62.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1Cn2ccc3c2cc(cc3)c4cc([nH]n4)N)CN5CCCCC5
InChI 
InChI=1S/C24H27N5/c25-24-15-22(26-27-24)21-9-8-20-10-13-29(23(20)14-21)17-19-6-4-18(5-7-19)16-28-11-2-1-3-12-28/h4-10,13-15H,1-3,11-12,16-17H2,(H3,25,26,27)
InChIKey 
VDYQWEHGAZCAGH-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)