Ligand profile

GB

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

Bound to: VK055_2269 — phosphonate ABC transporter, periplasmic phosphonate binding protein

Via homolog PDB 5o37 UniProt O69052 Formula CH₅O₃P
Mol. weight 96.02 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GB
PDB
5o37
UniProt (similar protein)
O69052
Target protein
VK055_2269

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 96.02 Da
LogP (Crippen) -0.21
H-bond donors 2
H-bond acceptors 1
TPSA 57.53 Ų
Rotatable bonds 0
Aromatic rings 0 / 0
Heavy atoms 5
Fraction sp³ C 1.00
Formula CH₅O₃P

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 57.5
  • −1 ≤ LogP ≤ 5 -0.21
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 96.0
  • LogP ≤ 5 -0.21
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 1
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 57.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CP(=O)(O)O
InChI 
InChI=1S/CH5O3P/c1-5(2,3)4/h1H3,(H2,2,3,4)
InChIKey 
YACKEPLHDIMKIO-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
PF12974

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_2269.

PDB 5

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

Ligand PDB entry

ZINC 11

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

Compound Similarity (Tanimoto)