Ligand profile

4H7

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

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

Via homolog PDB 4yqq UniProt P43912 Formula C₁₈H₂₃N₅O
Mol. weight 325.42 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
4H7
PDB
4yqq
UniProt (similar protein)
P43912
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 325.42 Da
LogP (Crippen) 1.54
H-bond donors 2
H-bond acceptors 5
TPSA 74.49 Ų
Rotatable bonds 5
Aromatic rings 2 / 3
Heavy atoms 24
Fraction sp³ C 0.33
Formula C₁₈H₂₃N₅O

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 74.5
  • −1 ≤ LogP ≤ 5 1.54
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 325.4
  • LogP ≤ 5 1.54
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 74.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN1CCN(CC1)c2ccccc2CNc3ccc(cn3)C(=O)N
InChI 
InChI=1S/C18H23N5O/c1-22-8-10-23(11-9-22)16-5-3-2-4-14(16)12-20-17-7-6-15(13-21-17)18(19)24/h2-7,13H,8-12H2,1H3,(H2,19,24)(H,20,21)
InChIKey 
BWXGFROIENPTFW-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)