Ligand profile

2YY

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

Bound to: KP13_02055 — Queuine tRNA-ribosyltransferase

Via homolog PDB 4q8w UniProt P28720 Formula C₁₈H₁₆N₆O₃
Mol. weight 364.37 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2YY
PDB
4q8w
UniProt (similar protein)
P28720
Target protein
KP13_02055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 364.37 Da
LogP (Crippen) 1.73
H-bond donors 5
H-bond acceptors 6
TPSA 149.78 Ų
Rotatable bonds 5
Aromatic rings 4 / 4
Heavy atoms 27
Fraction sp³ C 0.11
Formula C₁₈H₁₆N₆O₃

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 149.8
  • −1 ≤ LogP ≤ 5 1.73
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 364.4
  • LogP ≤ 5 1.73
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 149.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1CCNc2[nH]c3cc4c(cc3n2)N=C(NC4=O)N)C(=O)O
InChI 
InChI=1S/C18H16N6O3/c19-17-21-12-8-14-13(7-11(12)15(25)24-17)22-18(23-14)20-6-5-9-1-3-10(4-2-9)16(26)27/h1-4,7-8H,5-6H2,(H,26,27)(H2,20,22,23)(H3,19,21,24,25)
InChIKey 
TZNQMGFEWYPGDR-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)