Ligand profile

PON

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

Bound to: VK055_4203 — response regulator

Via homolog PDB 1ffw UniProt P0AE67 Formula H₃NO₆P₂²⁻
Mol. weight 174.97 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PON
PDB
1ffw
UniProt (similar protein)
P0AE67
Target protein
VK055_4203

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 174.97 Da
LogP (Crippen) -1.66
H-bond donors 3
H-bond acceptors 5
TPSA 136.73 Ų
Rotatable bonds 2
Aromatic rings 0 / 0
Heavy atoms 9
Fraction sp³ C 0.00
Formula H₃NO₆P₂²⁻

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 136.7
  • −1 ≤ LogP ≤ 5 -1.66
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 175.0
  • LogP ≤ 5 -1.66
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 136.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
N=[P@@](O)([O-])O[P@](=O)(O)[O-]
InChI 
InChI=1S/H4NO6P2/c1-8(2,3)7-9(4,5)6/h(H4-,1,2,3,4,5,6)/q-1/p-1
InChIKey 
VYBCVOULKDXKCH-UHFFFAOYSA-M

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
PF00072

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_4203.

PDB 6

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 6

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)