Ligand profile

CHEMBL5290255

Bioactivity hit from ChEMBL on a similar protein.

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

Via homolog UniProt P0A873 Formula C₁₉H₂₅N₅O₂
pchembl 7.43 ~37.2 nM
Mol. weight 355.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL5290255
UniProt (similar protein)
P0A873
pchembl
7.430 (~37.2 nM)
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 355.44 Da
LogP (Crippen) 1.22
H-bond donors 2
H-bond acceptors 5
TPSA 93.25 Ų
Rotatable bonds 5
Aromatic rings 2 / 4
Heavy atoms 26
Fraction sp³ C 0.53
Formula C₁₉H₂₅N₅O₂

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 93.3
  • −1 ≤ LogP ≤ 5 1.22
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 355.4
  • LogP ≤ 5 1.22
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 93.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN(C(=O)Cn1c(C2CC2)cc2cc(C(N)=O)cnc21)C1CCNCC1
InChI 
InChI=1S/C19H25N5O2/c1-23(15-4-6-21-7-5-15)17(25)11-24-16(12-2-3-12)9-13-8-14(18(20)26)10-22-19(13)24/h8-10,12,15,21H,2-7,11H2,1H3,(H2,20,26)
InChIKey 
ZDJRUJWXDYQCOC-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
ChEMBL
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 89

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 37

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)