Ligand profile

D3Y

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

Bound to: KP13_00617 — D-tyrosyl-tRNA(Tyr) deacylase

Via homolog PDB 4nbi UniProt Q8IIS0 Formula C₁₉H₂₃N₇O₅
Mol. weight 429.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
D3Y
PDB
4nbi
UniProt (similar protein)
Q8IIS0
Target protein
KP13_00617

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 429.44 Da
LogP (Crippen) -1.58
H-bond donors 6
H-bond acceptors 11
TPSA 194.66 Ų
Rotatable bonds 6
Aromatic rings 3 / 4
Heavy atoms 31
Fraction sp³ C 0.37
Formula C₁₉H₂₃N₇O₅

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 194.7
  • −1 ≤ LogP ≤ 5 -1.58
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 429.4
  • LogP ≤ 5 -1.58
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 194.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1C[C@H](C(=O)N[C@@H]2[C@H](O[C@H]([C@@H]2O)n3cnc4c3ncnc4N)CO)N)O
InChI 
InChI=1S/C19H23N7O5/c20-11(5-9-1-3-10(28)4-2-9)18(30)25-13-12(6-27)31-19(15(13)29)26-8-24-14-16(21)22-7-23-17(14)26/h1-4,7-8,11-13,15,19,27-29H,5-6,20H2,(H,25,30)(H2,21,22,23)/t11-,12-,13-,15-,19-/m1/s1
InChIKey 
GCCJIIJWAJOTAC-XDJZACDYSA-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
PF02580

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_00617.

PDB 3

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)