Ligand profile

WSA

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

Bound to: KP13_00709 — Tryptophanyl-tRNA synthetase

Via homolog PDB 2yy5 UniProt P75510 Formula C₂₁H₂₄N₈O₇S
Mol. weight 532.54 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
WSA
PDB
2yy5
UniProt (similar protein)
P75510
Target protein
KP13_00709

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 532.54 Da
LogP (Crippen) -1.54
H-bond donors 6
H-bond acceptors 13
TPSA 233.59 Ų
Rotatable bonds 8
Aromatic rings 4 / 5
Heavy atoms 37
Fraction sp³ C 0.33
Formula C₂₁H₂₄N₈O₇S

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 233.6
  • −1 ≤ LogP ≤ 5 -1.54
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 532.5
  • LogP ≤ 5 -1.54
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 233.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)N
InChI 
InChI=1S/C21H24N8O7S/c22-12(5-10-6-24-13-4-2-1-3-11(10)13)20(32)28-37(33,34)35-7-14-16(30)17(31)21(36-14)29-9-27-15-18(23)25-8-26-19(15)29/h1-4,6,8-9,12,14,16-17,21,24,30-31H,5,7,22H2,(H,28,32)(H2,23,25,26)/t12-,14+,16+,17+,21+/m0/s1
InChIKey 
RQAVKMXDGHWLGD-BFNSABJLSA-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 KP13_00709.

PDB 7

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)