Ligand profile

JPE

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

Bound to: KP13_04211 — Seryl-tRNA synthetase

Via homolog PDB 6r1o UniProt P0A8L1 Formula C₁₈H₂₂N₈O₈S
Mol. weight 510.49 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
JPE
PDB
6r1o
UniProt (similar protein)
P0A8L1
Target protein
KP13_04211

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 510.49 Da
LogP (Crippen) -3.21
H-bond donors 6
H-bond acceptors 15
TPSA 250.92 Ų
Rotatable bonds 8
Aromatic rings 3 / 4
Heavy atoms 35
Fraction sp³ C 0.39
Formula C₁₈H₂₂N₈O₈S

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 250.9
  • −1 ≤ LogP ≤ 5 -3.21
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 510.5
  • LogP ≤ 5 -3.21
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 250.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(cnc1)c2nc(c3c(n2)n(cn3)[C@H]4[C@@H]([C@@H]([C@H](O4)COS(=O)(=O)NC(=O)[C@H](CO)N)O)O)N
InChI 
InChI=1S/C18H22N8O8S/c19-9(5-27)17(30)25-35(31,32)33-6-10-12(28)13(29)18(34-10)26-7-22-11-14(20)23-15(24-16(11)26)8-2-1-3-21-4-8/h1-4,7,9-10,12-13,18,27-29H,5-6,19H2,(H,25,30)(H2,20,23,24)/t9-,10+,12+,13+,18+/m0/s1
InChIKey 
AJLUWRJYNKUFKX-OBXKABKQSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF00587

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_04211.

PDB 3

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

Ligand PDB entry

ChEMBL 4

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)