Ligand profile

X8Z

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

Bound to: KP13_03831 — Succinyl-diaminopimelate desuccinylase

Via homolog PDB 4pqa UniProt Q9JYL2 Formula C₉H₁₅NO₃S
Mol. weight 217.29 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
X8Z
PDB
4pqa
UniProt (similar protein)
Q9JYL2
Target protein
KP13_03831

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 217.29 Da
LogP (Crippen) 0.63
H-bond donors 2
H-bond acceptors 3
TPSA 57.61 Ų
Rotatable bonds 3
Aromatic rings 0 / 1
Heavy atoms 14
Fraction sp³ C 0.78
Formula C₉H₁₅NO₃S

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 57.6
  • −1 ≤ LogP ≤ 5 0.63
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 217.3
  • LogP ≤ 5 0.63
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 57.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H](CS)C(=O)N1CCC[C@H]1C(=O)O
InChI 
InChI=1S/C9H15NO3S/c1-6(5-14)8(11)10-4-2-3-7(10)9(12)13/h6-7,14H,2-5H2,1H3,(H,12,13)/t6-,7+/m1/s1
InChIKey 
FAKRSMQSSFJEIM-RQJHMYQMSA-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
PF01546' 'PF07687

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_03831.

PDB 3

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)