Ligand profile

A5P

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

Bound to: KP13_03839 — Transaldolase A

Via homolog PDB 3upb UniProt Q5NFX0 Formula C₅H₁₃O₈P
Mol. weight 232.13 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
A5P
PDB
3upb
UniProt (similar protein)
Q5NFX0
Target protein
KP13_03839

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 232.13 Da
LogP (Crippen) -2.83
H-bond donors 6
H-bond acceptors 6
TPSA 147.68 Ų
Rotatable bonds 6
Aromatic rings 0 / 0
Heavy atoms 14
Fraction sp³ C 1.00
Formula C₅H₁₃O₈P

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 147.7
  • −1 ≤ LogP ≤ 5 -2.83
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 232.1
  • LogP ≤ 5 -2.83
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 147.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)O
InChI 
InChI=1S/C5H13O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h3-9H,1-2H2,(H2,10,11,12)/t3-,4-,5+/m1/s1
InChIKey 
VJDOAZKNBQCAGE-WDCZJNDASA-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
PF00923

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_03839.

PDB 10

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)