Ligand profile

DPO

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

Bound to: VK055_2887 — adenylosuccinate synthase

Via homolog PDB 1kkf UniProt P0A7D4 Formula O₇P₂⁴⁻
Mol. weight 173.94 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DPO
PDB
1kkf
UniProt (similar protein)
P0A7D4
Target protein
VK055_2887

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 173.94 Da
LogP (Crippen) -3.34
H-bond donors 0
H-bond acceptors 7
TPSA 135.61 Ų
Rotatable bonds 2
Aromatic rings 0 / 0
Heavy atoms 9
Fraction sp³ C 0.00
Formula O₇P₂⁴⁻

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 135.6
  • −1 ≤ LogP ≤ 5 -3.34
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 173.9
  • LogP ≤ 5 -3.34
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 135.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[O-]P(=O)([O-])OP(=O)([O-])[O-]
InChI 
InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)/p-4
InChIKey 
XPPKVPWEQAFLFU-UHFFFAOYSA-J

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF00709

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_2887.

PDB 14

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)