Binder profile

PPI

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

Bound to: PA0927 — D-lactate dehydrogenase

Via homolog PDB 3kb6 UniProt O66939 C3H6O2
Mol. weight 74.08 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PPI
PDB
3kb6
UniProt (similar protein)
O66939
Target protein
PA0927

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 74.08 Da
LogP (Crippen) 0.48
H-bond donors 1
H-bond acceptors 1
TPSA 37.30 Ų
Rotatable bonds 1
Aromatic rings 0 / 0
Heavy atoms 5
Fraction sp³ C 0.67
Formula C3H6O2

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.

Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 74.1
  • LogP ≤ 5 0.48
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 1
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 37.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCC(=O)O
InChI 
InChI=1S/C3H6O2/c1-2-3(4)5/h2H2,1H3,(H,4,5)
InChIKey 
XBDQKXXYIPTUBI-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal TPW step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00389' 'PF02826

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA0927.

PDB 6

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 15

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)