Ligand profile

DW3

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

Bound to: KP13_03277 — 2-oxoglutarate dehydrogenase E1 component

Via homolog PDB 6kma UniProt A0A3Q0L1E1 Formula C₂H₄O₂
Mol. weight 60.05 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DW3
PDB
6kma
UniProt (similar protein)
A0A3Q0L1E1
Target protein
KP13_03277

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 60.05 Da
LogP (Crippen) -0.82
H-bond donors 1
H-bond acceptors 2
TPSA 37.30 Ų
Rotatable bonds 1
Aromatic rings 0 / 0
Heavy atoms 4
Fraction sp³ C 0.50
Formula C₂H₄O₂

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 37.3
  • −1 ≤ LogP ≤ 5 -0.82
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 60.1
  • LogP ≤ 5 -0.82
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 2
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 
C(C=O)O
InChI 
InChI=1S/C2H4O2/c3-1-2-4/h1,4H,2H2
InChIKey 
WGCNASOHLSPBMP-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
PF00676' 'PF02779

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_03277.

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)