Ligand profile

9WO

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

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

Via homolog PDB 6afk UniProt Q02RL6 Formula C₂₂H₂₂N₆O
Mol. weight 386.46 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9WO
PDB
6afk
UniProt (similar protein)
Q02RL6
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 386.46 Da
LogP (Crippen) 3.35
H-bond donors 3
H-bond acceptors 4
TPSA 89.70 Ų
Rotatable bonds 4
Aromatic rings 4 / 5
Heavy atoms 29
Fraction sp³ C 0.23
Formula C₂₂H₂₂N₆O

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 89.7
  • −1 ≤ LogP ≤ 5 3.35
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 386.5
  • LogP ≤ 5 3.35
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 89.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc2c(c1)cc([nH]2)C(=O)N[C@H]3CCCN(C3)c4cc(n[nH]4)c5ccncc5
InChI 
InChI=1S/C22H22N6O/c29-22(20-12-16-4-1-2-6-18(16)25-20)24-17-5-3-11-28(14-17)21-13-19(26-27-21)15-7-9-23-10-8-15/h1-2,4,6-10,12-13,17,25H,3,5,11,14H2,(H,24,29)(H,26,27)/t17-/m0/s1
InChIKey 
ZFKKLBZXLNWYEO-KRWDZBQOSA-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)