Ligand profile

21X

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

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

Via homolog PDB 4mcc UniProt P43912 Formula C₁₅H₁₄N₄O₂S
Mol. weight 314.37 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
21X
PDB
4mcc
UniProt (similar protein)
P43912
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 314.37 Da
LogP (Crippen) 1.37
H-bond donors 3
H-bond acceptors 5
TPSA 100.87 Ų
Rotatable bonds 4
Aromatic rings 3 / 3
Heavy atoms 22
Fraction sp³ C 0.13
Formula C₁₅H₁₄N₄O₂S

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 100.9
  • −1 ≤ LogP ≤ 5 1.37
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 314.4
  • LogP ≤ 5 1.37
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 100.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1CN)CNC(=O)c2csc3c2C(=O)NC=N3
InChI 
InChI=1S/C15H14N4O2S/c16-5-9-1-3-10(4-2-9)6-17-13(20)11-7-22-15-12(11)14(21)18-8-19-15/h1-4,7-8H,5-6,16H2,(H,17,20)(H,18,19,21)
InChIKey 
ZOJIHHOGTNVURO-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)