Ligand profile

2U9

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

Bound to: KP13_04673 — phenylalanyl-tRNA synthetase alpha subunit

Via homolog PDB 4p74 UniProt Q9I0A3 Formula C₁₆H₁₈N₂O₄S₂
Mol. weight 366.46 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2U9
PDB
4p74
UniProt (similar protein)
Q9I0A3
Target protein
KP13_04673

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 366.46 Da
LogP (Crippen) 1.95
H-bond donors 1
H-bond acceptors 6
TPSA 85.36 Ų
Rotatable bonds 5
Aromatic rings 2 / 3
Heavy atoms 24
Fraction sp³ C 0.38
Formula C₁₆H₁₈N₂O₄S₂

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 85.4
  • −1 ≤ LogP ≤ 5 1.95
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 366.5
  • LogP ≤ 5 1.95
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 85.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ccc(cc1)OCc2nc(cs2)C(=O)N[C@H]3CCS(=O)(=O)C3
InChI 
InChI=1S/C16H18N2O4S2/c1-11-2-4-13(5-3-11)22-8-15-18-14(9-23-15)16(19)17-12-6-7-24(20,21)10-12/h2-5,9,12H,6-8,10H2,1H3,(H,17,19)/t12-/m0/s1
InChIKey 
VINDBUONEPJWMV-LBPRGKRZSA-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
PF01409

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_04673.

PDB 7

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

Ligand PDB entry

ChEMBL 1

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)