Ligand profile

PG0

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

Bound to: KP13_05561 — Phosphoglycerate transport system sensor protein pgtB

Via homolog PDB 5ukv UniProt P71815 Formula C₅H₁₂O₃
Mol. weight 120.15 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PG0
PDB
5ukv
UniProt (similar protein)
P71815
Target protein
KP13_05561

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 120.15 Da
LogP (Crippen) -0.36
H-bond donors 1
H-bond acceptors 3
TPSA 38.69 Ų
Rotatable bonds 5
Aromatic rings 0 / 0
Heavy atoms 8
Fraction sp³ C 1.00
Formula C₅H₁₂O₃

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 38.7
  • −1 ≤ LogP ≤ 5 -0.36
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 120.1
  • LogP ≤ 5 -0.36
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 38.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COCCOCCO
InChI 
InChI=1S/C5H12O3/c1-7-4-5-8-3-2-6/h6H,2-5H2,1H3
InChIKey 
SBASXUCJHJRPEV-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
PF00512

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_05561.

PDB 2

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)