Ligand profile

3PY

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

Bound to: HT085_RS00085 — triose-phosphate isomerase

Via homolog PDB 1o5x UniProt Q07412 Formula C₃H₄O₄
Mol. weight 104.06 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3PY
PDB
1o5x
UniProt (similar protein)
Q07412
Target protein
HT085_RS00085

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 104.06 Da
LogP (Crippen) -1.37
H-bond donors 2
H-bond acceptors 3
TPSA 74.60 Ų
Rotatable bonds 2
Aromatic rings 0 / 0
Heavy atoms 7
Fraction sp³ C 0.33
Formula C₃H₄O₄

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 74.6
  • −1 ≤ LogP ≤ 5 -1.37
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 104.1
  • LogP ≤ 5 -1.37
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 74.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(C(=O)C(=O)O)O
InChI 
InChI=1S/C3H4O4/c4-1-2(5)3(6)7/h4H,1H2,(H,6,7)
InChIKey 
HHDDCCUIIUWNGJ-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
PF00121

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to HT085_RS00085.

PDB 9

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)