Ligand profile

CHEMBL5289815

Bioactivity hit from ChEMBL on a similar protein.

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

Via homolog UniProt P0A873 Formula C₁₇H₂₁N₅O
pchembl 6.51 ~309.0 nM
Mol. weight 311.39 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL5289815
UniProt (similar protein)
P0A873
pchembl
6.510 (~309.0 nM)
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 311.39 Da
LogP (Crippen) 1.20
H-bond donors 3
H-bond acceptors 5
TPSA 83.28 Ų
Rotatable bonds 5
Aromatic rings 2 / 3
Heavy atoms 23
Fraction sp³ C 0.29
Formula C₁₇H₂₁N₅O

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 83.3
  • −1 ≤ LogP ≤ 5 1.20
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 311.4
  • LogP ≤ 5 1.20
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 83.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
NC(=O)c1ccc(NCc2cccc(N3CCNCC3)c2)nc1
InChI 
InChI=1S/C17H21N5O/c18-17(23)14-4-5-16(21-12-14)20-11-13-2-1-3-15(10-13)22-8-6-19-7-9-22/h1-5,10,12,19H,6-9,11H2,(H2,18,23)(H,20,21)
InChIKey 
JNTHNCJDQUJFLH-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)