Ligand profile

8X1

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

Bound to: KP13_03562 — Glutamyl-tRNA synthetase

Via homolog PDB 5v58 UniProt P07814 Formula C₁₄H₁₉N₇O₇S
Mol. weight 429.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
8X1
PDB
5v58
UniProt (similar protein)
P07814
Target protein
KP13_03562

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 429.42 Da
LogP (Crippen) -3.23
H-bond donors 5
H-bond acceptors 13
TPSA 203.81 Ų
Rotatable bonds 6
Aromatic rings 2 / 4
Heavy atoms 29
Fraction sp³ C 0.57
Formula C₁₄H₁₉N₇O₇S

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 203.8
  • −1 ≤ LogP ≤ 5 -3.23
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 429.4
  • LogP ≤ 5 -3.23
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 203.8
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]4CCN4)O)O)N
InChI 
InChI=1S/C14H19N7O7S/c15-11-8-12(18-4-17-11)21(5-19-8)14-10(23)9(22)7(28-14)3-27-29(25,26)20-13(24)6-1-2-16-6/h4-7,9-10,14,16,22-23H,1-3H2,(H,20,24)(H2,15,17,18)/t6-,7+,9+,10+,14+/m0/s1
InChIKey 
DQFRXHHGQUUTOL-XLZJSAHRSA-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
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_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)