Ligand profile

P2D

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

Bound to: KP13_04881 — Transaldolase 1

Via homolog PDB 4s1f UniProt P78055 Formula C₅H₈O₂
Mol. weight 100.12 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
P2D
PDB
4s1f
UniProt (similar protein)
P78055
Target protein
KP13_04881

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 100.12 Da
LogP (Crippen) 0.55
H-bond donors 0
H-bond acceptors 2
TPSA 34.14 Ų
Rotatable bonds 2
Aromatic rings 0 / 0
Heavy atoms 7
Fraction sp³ C 0.60
Formula C₅H₈O₂

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 34.1
  • −1 ≤ LogP ≤ 5 0.55
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 100.1
  • LogP ≤ 5 0.55
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 34.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)CC(=O)C
InChI 
InChI=1S/C5H8O2/c1-4(6)3-5(2)7/h3H2,1-2H3
InChIKey 
YRKCREAYFQTBPV-UHFFFAOYSA-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_04881.

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)