Ligand profile

4GZ

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

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

Via homolog PDB 4yqd UniProt P43912 Formula C₂₃H₃₀N₄O₂
Mol. weight 394.52 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
4GZ
PDB
4yqd
UniProt (similar protein)
P43912
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 394.52 Da
LogP (Crippen) 3.67
H-bond donors 3
H-bond acceptors 4
TPSA 97.11 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 29
Fraction sp³ C 0.43
Formula C₂₃H₃₀N₄O₂

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 97.1
  • −1 ≤ LogP ≤ 5 3.67
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 394.5
  • LogP ≤ 5 3.67
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 97.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cccc(c1)C(=O)NCCC2(CCCCC2)CNc3ccc(cn3)C(=O)N
InChI 
InChI=1S/C23H30N4O2/c1-17-6-5-7-18(14-17)22(29)25-13-12-23(10-3-2-4-11-23)16-27-20-9-8-19(15-26-20)21(24)28/h5-9,14-15H,2-4,10-13,16H2,1H3,(H2,24,28)(H,25,29)(H,26,27)
InChIKey 
BAQVREQCCQUZHH-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)