Ligand profile

4GN

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

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

Via homolog PDB 4yqa UniProt P43912 Formula C₁₂H₁₇N₃O
Mol. weight 219.29 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
4GN
PDB
4yqa
UniProt (similar protein)
P43912
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 219.29 Da
LogP (Crippen) 1.78
H-bond donors 2
H-bond acceptors 3
TPSA 68.01 Ų
Rotatable bonds 4
Aromatic rings 1 / 2
Heavy atoms 16
Fraction sp³ C 0.50
Formula C₁₂H₁₇N₃O

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 68.0
  • −1 ≤ LogP ≤ 5 1.78
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 219.3
  • LogP ≤ 5 1.78
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 68.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ncc1C(=O)N)NCC2CCCC2
InChI 
InChI=1S/C12H17N3O/c13-12(16)10-5-6-11(15-8-10)14-7-9-3-1-2-4-9/h5-6,8-9H,1-4,7H2,(H2,13,16)(H,14,15)
InChIKey 
KSUTVZCNRWWYFG-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)