Ligand profile

2YX

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

Bound to: KP13_02055 — Queuine tRNA-ribosyltransferase

Via homolog PDB 4q8v UniProt P28720 Formula C₁₈H₁₅N₇O
Mol. weight 345.37 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2YX
PDB
4q8v
UniProt (similar protein)
P28720
Target protein
KP13_02055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 345.37 Da
LogP (Crippen) 1.91
H-bond donors 4
H-bond acceptors 6
TPSA 136.27 Ų
Rotatable bonds 4
Aromatic rings 4 / 4
Heavy atoms 26
Fraction sp³ C 0.11
Formula C₁₈H₁₅N₇O

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 136.3
  • −1 ≤ LogP ≤ 5 1.91
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 345.4
  • LogP ≤ 5 1.91
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 136.3
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#N
InChI 
InChI=1S/C18H15N7O/c19-9-11-3-1-10(2-4-11)5-6-21-18-23-14-7-12-13(8-15(14)24-18)22-17(20)25-16(12)26/h1-4,7-8H,5-6H2,(H2,21,23,24)(H3,20,22,25,26)
InChIKey 
NYFZULJQMISTPE-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)