Ligand profile

2YL

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

Bound to: KP13_02055 — Queuine tRNA-ribosyltransferase

Via homolog PDB 4q4m UniProt P28720 Formula C₉H₈N₄O
Mol. weight 188.19 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2YL
PDB
4q4m
UniProt (similar protein)
P28720
Target protein
KP13_02055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 188.19 Da
LogP (Crippen) 0.41
H-bond donors 2
H-bond acceptors 4
TPSA 84.66 Ų
Rotatable bonds 1
Aromatic rings 2 / 2
Heavy atoms 14
Fraction sp³ C 0.00
Formula C₉H₈N₄O

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 84.7
  • −1 ≤ LogP ≤ 5 0.41
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 188.2
  • LogP ≤ 5 0.41
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 84.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)C2=NC(=O)NC(=N2)N
InChI 
InChI=1S/C9H8N4O/c10-8-11-7(12-9(14)13-8)6-4-2-1-3-5-6/h1-5H,(H3,10,11,12,13,14)
InChIKey 
ZBKCUYOBOGCDKC-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)