Ligand profile

PED

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

Bound to: VK055_0907 — hypothetical protein

Via homolog PDB 6kij UniProt P76318 Formula C₅H₁₃O₆P
Mol. weight 200.13 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PED
PDB
6kij
UniProt (similar protein)
P76318
Target protein
VK055_0907

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 200.13 Da
LogP (Crippen) -0.77
H-bond donors 4
H-bond acceptors 4
TPSA 107.22 Ų
Rotatable bonds 5
Aromatic rings 0 / 0
Heavy atoms 12
Fraction sp³ C 1.00
Formula C₅H₁₃O₆P

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 107.2
  • −1 ≤ LogP ≤ 5 -0.77
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 200.1
  • LogP ≤ 5 -0.77
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 107.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC[C@@H]([C@@H](COP(=O)(O)O)O)O
InChI 
InChI=1S/C5H13O6P/c1-2-4(6)5(7)3-11-12(8,9)10/h4-7H,2-3H2,1H3,(H2,8,9,10)/t4-,5+/m0/s1
InChIKey 
FQKLTSRHTQGSQZ-CRCLSJGQSA-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
PF02586

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_0907.

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)