Ligand profile

4H3

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

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

Via homolog PDB 4yqn UniProt P43912 Formula C₁₂H₁₇N₃O₃
Mol. weight 251.29 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
4H3
PDB
4yqn
UniProt (similar protein)
P43912
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 251.29 Da
LogP (Crippen) -0.28
H-bond donors 4
H-bond acceptors 5
TPSA 108.47 Ų
Rotatable bonds 4
Aromatic rings 1 / 2
Heavy atoms 18
Fraction sp³ C 0.50
Formula C₁₂H₁₇N₃O₃

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 108.5
  • −1 ≤ LogP ≤ 5 -0.28
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 251.3
  • LogP ≤ 5 -0.28
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 108.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ncc1C(=O)N)N[C@@H]2C[C@@H]([C@H](C2)O)CO
InChI 
InChI=1S/C12H17N3O3/c13-12(18)7-1-2-11(14-5-7)15-9-3-8(6-16)10(17)4-9/h1-2,5,8-10,16-17H,3-4,6H2,(H2,13,18)(H,14,15)/t8-,9-,10+/m1/s1
InChIKey 
OOPBXYPWRQVSFZ-BBBLOLIVSA-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)