Ligand profile

SXA

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

Bound to: KP13_00363 — LpxA-like domain-containing transferase

Via homolog PDB 6x3c UniProt P26839 Formula C₁₃H₂₅N₂O₈PS
Mol. weight 400.39 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SXA
PDB
6x3c
UniProt (similar protein)
P26839
Target protein
KP13_00363

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 400.39 Da
LogP (Crippen) -0.61
H-bond donors 5
H-bond acceptors 7
TPSA 162.26 Ų
Rotatable bonds 11
Aromatic rings 0 / 0
Heavy atoms 25
Fraction sp³ C 0.77
Formula C₁₃H₂₅N₂O₈PS

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 162.3
  • −1 ≤ LogP ≤ 5 -0.61
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 400.4
  • LogP ≤ 5 -0.61
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 162.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)SCCNC(=O)CCNC(=O)[C@H](C(C)(C)COP(=O)(O)O)O
InChI 
InChI=1S/C13H25N2O8PS/c1-9(16)25-7-6-14-10(17)4-5-15-12(19)11(18)13(2,3)8-23-24(20,21)22/h11,18H,4-8H2,1-3H3,(H,14,17)(H,15,19)(H2,20,21,22)/t11-/m1/s1
InChIKey 
AJFWMDFTVVFMHY-LLVKDONJSA-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
PF00132

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_00363.

PDB 15

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)