Ligand profile

9X7

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

Bound to: KP13_00665 — Glucose-1-phosphate adenylyltransferase

Via homolog PDB 5w5t UniProt P39669 Formula C₅H₈O₃
Mol. weight 116.12 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9X7
PDB
5w5t
UniProt (similar protein)
P39669
Target protein
KP13_00665

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 116.12 Da
LogP (Crippen) 0.14
H-bond donors 0
H-bond acceptors 3
TPSA 43.37 Ų
Rotatable bonds 2
Aromatic rings 0 / 0
Heavy atoms 8
Fraction sp³ C 0.60
Formula C₅H₈O₃

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 43.4
  • −1 ≤ LogP ≤ 5 0.14
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 116.1
  • LogP ≤ 5 0.14
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 43.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCOC(=O)C(=O)C
InChI 
InChI=1S/C5H8O3/c1-3-8-5(7)4(2)6/h3H2,1-2H3
InChIKey 
XXRCUYVCPSWGCC-UHFFFAOYSA-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
PF00483

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_00665.

PDB 30

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)