Ligand profile

4H9

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

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

Via homolog PDB 4yqs UniProt P43912 Formula C₁₀H₁₀N₄O₂
Mol. weight 218.22 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
4H9
PDB
4yqs
UniProt (similar protein)
P43912
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 218.22 Da
LogP (Crippen) 0.56
H-bond donors 1
H-bond acceptors 6
TPSA 83.03 Ų
Rotatable bonds 2
Aromatic rings 2 / 2
Heavy atoms 16
Fraction sp³ C 0.10
Formula C₁₀H₁₀N₄O₂

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 83.0
  • −1 ≤ LogP ≤ 5 0.56
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 218.2
  • LogP ≤ 5 0.56
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 83.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccc(cc1)C(=O)n2c(ncn2)N
InChI 
InChI=1S/C10H10N4O2/c1-16-8-4-2-7(3-5-8)9(15)14-10(11)12-6-13-14/h2-6H,1H3,(H2,11,12,13)
InChIKey 
MDFWUVGMSOBSKJ-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)