Ligand profile

ZINC70556875

Virtual-screening candidate from ZINC.

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

Via homolog UniProt P0A873 Formula C₁₃H₁₇N₃O₃
Tanimoto 0.72
Mol. weight 263.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC70556875
UniProt (similar protein)
P0A873
Tanimoto
0.718
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 263.30 Da
LogP (Crippen) 1.24
H-bond donors 3
H-bond acceptors 4
TPSA 105.31 Ų
Rotatable bonds 4
Aromatic rings 1 / 2
Heavy atoms 19
Fraction sp³ C 0.46
Formula C₁₃H₁₇N₃O₃

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 105.3
  • −1 ≤ LogP ≤ 5 1.24
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 263.3
  • LogP ≤ 5 1.24
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 105.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
NC(=O)c1ccc(N[C@@H]2CCC[C@H](C(=O)O)C2)nc1
InChI 
InChI=1S/C13H17N3O3/c14-12(17)9-4-5-11(15-7-9)16-10-3-1-2-8(6-10)13(18)19/h4-5,7-8,10H,1-3,6H2,(H2,14,17)(H,15,16)(H,18,19)/t8-,10+/m0/s1
InChIKey 
XELXEIVRJJWGFU-WCBMZHEXSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Query
4GO
Homolog
P0A873

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 89

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 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)