Ligand profile

2YO

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

Bound to: KP13_02055 — Queuine tRNA-ribosyltransferase

Via homolog PDB 4q4p UniProt P28720 Formula C₁₆H₂₀N₆O
Mol. weight 312.38 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2YO
PDB
4q4p
UniProt (similar protein)
P28720
Target protein
KP13_02055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 312.38 Da
LogP (Crippen) 1.70
H-bond donors 3
H-bond acceptors 5
TPSA 89.70 Ų
Rotatable bonds 4
Aromatic rings 3 / 4
Heavy atoms 23
Fraction sp³ C 0.44
Formula C₁₆H₂₀N₆O

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 1.70
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 312.4
  • LogP ≤ 5 1.70
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
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 
c1c2c(cc3c1nc([nH]3)NCCN4CCCCC4)NC=NC2=O
InChI 
InChI=1S/C16H20N6O/c23-15-11-8-13-14(9-12(11)18-10-19-15)21-16(20-13)17-4-7-22-5-2-1-3-6-22/h8-10H,1-7H2,(H2,17,20,21)(H,18,19,23)
InChIKey 
NFLZHTAOFKJMSG-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)