Ligand profile

4GY

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

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

Via homolog PDB 4yqg UniProt P43912 Formula C₁₀H₁₆N₄O₂
Mol. weight 224.26 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
4GY
PDB
4yqg
UniProt (similar protein)
P43912
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 224.26 Da
LogP (Crippen) 0.96
H-bond donors 2
H-bond acceptors 5
TPSA 94.04 Ų
Rotatable bonds 3
Aromatic rings 1 / 2
Heavy atoms 16
Fraction sp³ C 0.70
Formula C₁₀H₁₆N₄O₂

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 94.0
  • −1 ≤ LogP ≤ 5 0.96
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 224.3
  • LogP ≤ 5 0.96
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 94.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1CCC(CC1)CNC(=O)c2c(non2)N
InChI 
InChI=1S/C10H16N4O2/c11-9-8(13-16-14-9)10(15)12-6-7-4-2-1-3-5-7/h7H,1-6H2,(H2,11,14)(H,12,15)
InChIKey 
LMUMGZXENBDFGR-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)