Ligand profile

Y3U

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

Bound to: HT085_RS00335 — tyrosine--tRNA ligase

Via homolog PDB 6hb7 UniProt P0AGJ9 Formula C₁₉H₂₄N₄O₁₀S
Mol. weight 500.49 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
Y3U
PDB
6hb7
UniProt (similar protein)
P0AGJ9
Target protein
HT085_RS00335

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 500.49 Da
LogP (Crippen) -3.18
H-bond donors 5
H-bond acceptors 13
TPSA 212.41 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 34
Fraction sp³ C 0.42
Formula C₁₉H₂₄N₄O₁₀S

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 212.4
  • −1 ≤ LogP ≤ 5 -3.18
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 500.5
  • LogP ≤ 5 -3.18
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 212.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN1C(=O)C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COS(=O)(=O)NC(=O)[C@H](Cc3ccc(cc3)O)N)O)O
InChI 
InChI=1S/C19H24N4O10S/c1-22-14(25)6-7-23(19(22)29)18-16(27)15(26)13(33-18)9-32-34(30,31)21-17(28)12(20)8-10-2-4-11(24)5-3-10/h2-7,12-13,15-16,18,24,26-27H,8-9,20H2,1H3,(H,21,28)/t12-,13+,15+,16+,18+/m0/s1
InChIKey 
JZICRHJSYJTEMP-IQNGCQKYSA-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
PF00579

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to HT085_RS00335.

PDB 7

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

Ligand PDB entry

ChEMBL 7

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)