Ligand profile

2YW

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

Bound to: KP13_02055 — Queuine tRNA-ribosyltransferase

Via homolog PDB 4q8u UniProt P28720 Formula C₁₉H₁₈N₆O₃
Mol. weight 378.39 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2YW
PDB
4q8u
UniProt (similar protein)
P28720
Target protein
KP13_02055

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 378.39 Da
LogP (Crippen) 1.82
H-bond donors 4
H-bond acceptors 7
TPSA 138.78 Ų
Rotatable bonds 5
Aromatic rings 4 / 4
Heavy atoms 28
Fraction sp³ C 0.16
Formula C₁₉H₁₈N₆O₃

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 138.8
  • −1 ≤ LogP ≤ 5 1.82
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 378.4
  • LogP ≤ 5 1.82
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 138.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COC(=O)c1ccc(cc1)CCNc2[nH]c3cc4c(cc3n2)N=C(NC4=O)N
InChI 
InChI=1S/C19H18N6O3/c1-28-17(27)11-4-2-10(3-5-11)6-7-21-19-23-14-8-12-13(9-15(14)24-19)22-18(20)25-16(12)26/h2-5,8-9H,6-7H2,1H3,(H2,21,23,24)(H3,20,22,25,26)
InChIKey 
OYIIDOTURROWKC-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)