Ligand profile

RB0

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

Bound to: VK055_2774 — bacterial extracellular solute-binding family protein

Via homolog PDB 5iai UniProt B9JM84 Formula C₅H₁₂O₅
Mol. weight 152.15 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RB0
PDB
5iai
UniProt (similar protein)
B9JM84
Target protein
VK055_2774

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 152.15 Da
LogP (Crippen) -2.95
H-bond donors 5
H-bond acceptors 5
TPSA 101.15 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 10
Fraction sp³ C 1.00
Formula C₅H₁₂O₅

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 101.2
  • −1 ≤ LogP ≤ 5 -2.95
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 152.1
  • LogP ≤ 5 -2.95
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 101.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@H](C([C@H](CO)O)O)O)O
InChI 
InChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4+,5?
InChIKey 
HEBKCHPVOIAQTA-NGQZWQHPSA-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
PF01547

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_2774.

PDB 7

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)