Ligand profile

GSU

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

Bound to: KP13_03562 — Glutamyl-tRNA synthetase

Via homolog PDB 2cv2 UniProt P27000 Formula C₁₅H₂₁N₇O₉S
Mol. weight 475.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GSU
PDB
2cv2
UniProt (similar protein)
P27000
Target protein
KP13_03562

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 475.44 Da
LogP (Crippen) -3.40
H-bond donors 6
H-bond acceptors 14
TPSA 255.10 Ų
Rotatable bonds 9
Aromatic rings 2 / 3
Heavy atoms 32
Fraction sp³ C 0.53
Formula C₁₅H₂₁N₇O₉S

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 255.1
  • −1 ≤ LogP ≤ 5 -3.40
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 475.4
  • LogP ≤ 5 -3.40
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 255.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COS(=O)(=O)NC(=O)[C@H](CCC(=O)O)N)O)O)N
InChI 
InChI=1S/C15H21N7O9S/c16-6(1-2-8(23)24)14(27)21-32(28,29)30-3-7-10(25)11(26)15(31-7)22-5-20-9-12(17)18-4-19-13(9)22/h4-7,10-11,15,25-26H,1-3,16H2,(H,21,27)(H,23,24)(H2,17,18,19)/t6-,7+,10+,11+,15+/m0/s1
InChIKey 
YBRKRYFZKHICLS-WERHYGNASA-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
PF00749

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_03562.

PDB 9

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

Ligand PDB entry

ChEMBL 3

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)