Ligand profile

3GR

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

Bound to: VK055_4865 — 2-keto-3-deoxy-L-rhamnonate aldolase

Via homolog PDB 4b5s UniProt B1IS70 Formula C₃H₆O₃
Mol. weight 90.08 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3GR
PDB
4b5s
UniProt (similar protein)
B1IS70
Target protein
VK055_4865

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 90.08 Da
LogP (Crippen) -1.46
H-bond donors 2
H-bond acceptors 3
TPSA 57.53 Ų
Rotatable bonds 2
Aromatic rings 0 / 0
Heavy atoms 6
Fraction sp³ C 0.67
Formula C₃H₆O₃

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 57.5
  • −1 ≤ LogP ≤ 5 -1.46
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 90.1
  • LogP ≤ 5 -1.46
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 57.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@H](C=O)O)O
InChI 
InChI=1S/C3H6O3/c4-1-3(6)2-5/h1,3,5-6H,2H2/t3-/m0/s1
InChIKey 
MNQZXJOMYWMBOU-VKHMYHEASA-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
PF03328

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to VK055_4865.

PDB 6

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

Ligand PDB entry

ZINC 6

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

Compound Similarity (Tanimoto)