Binder profile

R5P

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

Bound to: PA4670 — ribose-phosphate pyrophosphokinase

Via homolog PDB 1u9z UniProt Q58761 C5H11O8P
Mol. weight 230.11 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
R5P
PDB
1u9z
UniProt (similar protein)
Q58761
Target protein
PA4670

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 230.11 Da
LogP (Crippen) -2.62
H-bond donors 5
H-bond acceptors 6
TPSA 144.52 Ų
Rotatable bonds 6
Aromatic rings 0 / 0
Heavy atoms 14
Fraction sp³ C 0.80
Formula C5H11O8P

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.

Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 230.1
  • LogP ≤ 5 -2.62
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 144.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(C(C(C(C=O)O)O)O)OP(=O)(O)O
InChI 
InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h1,3-5,7-9H,2H2,(H2,10,11,12)
InChIKey 
PPQRONHOSHZGFQ-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
PF00156

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA4670.

PDB 1

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)