Ligand profile

CHEMBL5276347

Bioactivity hit from ChEMBL on a similar protein.

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

Via homolog UniProt P0A873 Formula C₂₀H₂₇N₅O₂
pchembl 7.41 ~38.9 nM
Mol. weight 369.47 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL5276347
UniProt (similar protein)
P0A873
pchembl
7.410 (~38.9 nM)
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 369.47 Da
LogP (Crippen) 1.57
H-bond donors 1
H-bond acceptors 5
TPSA 84.46 Ų
Rotatable bonds 5
Aromatic rings 2 / 4
Heavy atoms 27
Fraction sp³ C 0.55
Formula C₂₀H₂₇N₅O₂

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 84.5
  • −1 ≤ LogP ≤ 5 1.57
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 369.5
  • LogP ≤ 5 1.57
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 84.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN1CCC(N(C)C(=O)Cn2c(C3CC3)cc3cc(C(N)=O)cnc32)CC1
InChI 
InChI=1S/C20H27N5O2/c1-23-7-5-16(6-8-23)24(2)18(26)12-25-17(13-3-4-13)10-14-9-15(19(21)27)11-22-20(14)25/h9-11,13,16H,3-8,12H2,1-2H3,(H2,21,27)
InChIKey 
ZRYBTEHWDKITLC-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)