Ligand profile

XDA

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

Bound to: VK055_3487 — SMP-30/Gluconolaconase/LRE-like region family protein

Via homolog PDB 4o5t UniProt Q7SIG4 Formula C₂₀H₂₈N₃O₈P
Mol. weight 469.43 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
XDA
PDB
4o5t
UniProt (similar protein)
Q7SIG4
Target protein
VK055_3487

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 469.43 Da
LogP (Crippen) 1.17
H-bond donors 4
H-bond acceptors 6
TPSA 154.50 Ų
Rotatable bonds 9
Aromatic rings 1 / 2
Heavy atoms 32
Fraction sp³ C 0.45
Formula C₂₀H₂₈N₃O₈P

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 154.5
  • −1 ≤ LogP ≤ 5 1.17
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 469.4
  • LogP ≤ 5 1.17
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 154.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN(C)C(=O)[C@H]1CCC=C[C@H]1NC(=O)OCc2ccc(cc2)C(=O)NCCOP(=O)(O)O
InChI 
InChI=1S/C20H28N3O8P/c1-23(2)19(25)16-5-3-4-6-17(16)22-20(26)30-13-14-7-9-15(10-8-14)18(24)21-11-12-31-32(27,28)29/h4,6-10,16-17H,3,5,11-13H2,1-2H3,(H,21,24)(H,22,26)(H2,27,28,29)/t16-,17+/m0/s1
InChIKey 
MBWSSOJOAZHENI-DLBZAZTESA-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
PF08450

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_3487.

PDB 4

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)