Ligand profile

3LR

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

Bound to: VK055_4863 — L-rhamnonate dehydratase

Via homolog PDB 3cxo UniProt Q8ZNF9 Formula C₆H₁₂O₅
Mol. weight 164.16 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3LR
PDB
3cxo
UniProt (similar protein)
Q8ZNF9
Target protein
VK055_4863

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 164.16 Da
LogP (Crippen) -1.44
H-bond donors 4
H-bond acceptors 4
TPSA 97.99 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 11
Fraction sp³ C 0.83
Formula C₆H₁₂O₅

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 98.0
  • −1 ≤ LogP ≤ 5 -1.44
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 164.2
  • LogP ≤ 5 -1.44
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 98.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]([C@@H](C[C@H](C(=O)O)O)O)O
InChI 
InChI=1S/C6H12O5/c1-3(7)4(8)2-5(9)6(10)11/h3-5,7-9H,2H2,1H3,(H,10,11)/t3-,4+,5+/m0/s1
InChIKey 
RJZYGPZBSUBNEJ-VPENINKCSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF13378

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_4863.

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)