Ligand profile

810

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

Bound to: KP13_02055 — Queuine tRNA-ribosyltransferase

Via homolog PDB 5jgm UniProt P28720 Formula C₁₃H₁₄N₆O₃
Mol. weight 302.29 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
810
PDB
5jgm
UniProt (similar protein)
P28720
Target protein
KP13_02055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 302.29 Da
LogP (Crippen) 1.41
H-bond donors 4
H-bond acceptors 6
TPSA 124.79 Ų
Rotatable bonds 3
Aromatic rings 3 / 3
Heavy atoms 22
Fraction sp³ C 0.23
Formula C₁₃H₁₄N₆O₃

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 124.8
  • −1 ≤ LogP ≤ 5 1.41
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 302.3
  • LogP ≤ 5 1.41
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 124.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCOC(=O)NC1=Nc2cc3c(cc2C(=O)N1)[nH]c(n3)NC
InChI 
InChI=1S/C13H14N6O3/c1-3-22-13(21)19-12-15-7-5-9-8(16-11(14-2)17-9)4-6(7)10(20)18-12/h4-5H,3H2,1-2H3,(H2,14,16,17)(H2,15,18,19,20,21)
InChIKey 
KXOJIFFEGXMDQZ-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
PF01702

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_02055.

PDB 60

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 5

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)