Ligand profile

21W

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

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

Via homolog PDB 4mcb UniProt P43912 Formula C₁₉H₁₈N₆O₂S
Mol. weight 394.46 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
21W
PDB
4mcb
UniProt (similar protein)
P43912
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 394.46 Da
LogP (Crippen) 1.93
H-bond donors 4
H-bond acceptors 6
TPSA 115.56 Ų
Rotatable bonds 7
Aromatic rings 4 / 4
Heavy atoms 28
Fraction sp³ C 0.16
Formula C₁₉H₁₈N₆O₂S

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 115.6
  • −1 ≤ LogP ≤ 5 1.93
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 394.5
  • LogP ≤ 5 1.93
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 115.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1CNCc2[nH]ccn2)CNC(=O)c3csc4c3C(=O)NC=N4
InChI 
InChI=1S/C19H18N6O2S/c26-17(14-10-28-19-16(14)18(27)24-11-25-19)23-8-13-3-1-12(2-4-13)7-20-9-15-21-5-6-22-15/h1-6,10-11,20H,7-9H2,(H,21,22)(H,23,26)(H,24,25,27)
InChIKey 
RLANZYKQCHLLJS-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)