Ligand profile

4H8

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

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

Via homolog PDB 4yqt UniProt P43912 Formula C₁₀H₁₇N₅O
Mol. weight 223.28 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
4H8
PDB
4yqt
UniProt (similar protein)
P43912
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 223.28 Da
LogP (Crippen) 0.62
H-bond donors 3
H-bond acceptors 5
TPSA 106.92 Ų
Rotatable bonds 3
Aromatic rings 1 / 1
Heavy atoms 16
Fraction sp³ C 0.50
Formula C₁₀H₁₇N₅O

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 106.9
  • −1 ≤ LogP ≤ 5 0.62
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 223.3
  • LogP ≤ 5 0.62
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 106.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(C)CNc1ncc(c(n1)N)C(=O)N
InChI 
InChI=1S/C10H17N5O/c1-10(2,3)5-14-9-13-4-6(8(12)16)7(11)15-9/h4H,5H2,1-3H3,(H2,12,16)(H3,11,13,14,15)
InChIKey 
PYEPYUBHFUICHO-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)