Binder profile

DMG

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

Bound to: PA5304 — D-amino acid dehydrogenase small subunit

Via homolog PDB 1vrq UniProt Q50LF2 C4H9NO2
Mol. weight 103.12 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DMG
PDB
1vrq
UniProt (similar protein)
Q50LF2
Target protein
PA5304

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 103.12 Da
LogP (Crippen) -0.37
H-bond donors 1
H-bond acceptors 2
TPSA 40.54 Ų
Rotatable bonds 2
Aromatic rings 0 / 0
Heavy atoms 7
Fraction sp³ C 0.75
Formula C4H9NO2

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 103.1
  • LogP ≤ 5 -0.37
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 40.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN(C)CC(=O)O
InChI 
InChI=1S/C4H9NO2/c1-5(2)3-4(6)7/h3H2,1-2H3,(H,6,7)
InChIKey 
FFDGPVCHZBVARC-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
PF01266

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA5304.

PDB 8

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)