Ligand profile

RB5

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

Bound to: KP13_04882 — putative ribose-5-phosphate isomerase B

Via homolog PDB 3ph3 UniProt A3DIL8 Formula C₅H₁₀O₅
Mol. weight 150.13 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RB5
PDB
3ph3
UniProt (similar protein)
A3DIL8
Target protein
KP13_04882

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 150.13 Da
LogP (Crippen) -2.74
H-bond donors 4
H-bond acceptors 5
TPSA 97.99 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 10
Fraction sp³ C 0.80
Formula C₅H₁₀O₅

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 -2.74
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 150.1
  • LogP ≤ 5 -2.74
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
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@H](C=O)O)O)O)O
InChI 
InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h1,3-5,7-10H,2H2/t3-,4+,5-/m0/s1
InChIKey 
PYMYPHUHKUWMLA-LMVFSUKVSA-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
PF02502

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_04882.

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)