Ligand profile

DI9

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 2gvv UniProt Q7SIG4 Formula C₁₀H₂₀NO₃P
Mol. weight 233.25 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DI9
PDB
2gvv
UniProt (similar protein)
Q7SIG4
Target protein
VK055_3487

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 233.25 Da
LogP (Crippen) 2.97
H-bond donors 1
H-bond acceptors 3
TPSA 61.55 Ų
Rotatable bonds 4
Aromatic rings 0 / 2
Heavy atoms 15
Fraction sp³ C 1.00
Formula C₁₀H₂₀NO₃P

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 61.5
  • −1 ≤ LogP ≤ 5 2.97
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 233.2
  • LogP ≤ 5 2.97
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 61.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1CCC(C1)OP(=O)(N)OC2CCCC2
InChI 
InChI=1S/C10H20NO3P/c11-15(12,13-9-5-1-2-6-9)14-10-7-3-4-8-10/h9-10H,1-8H2,(H2,11,12)
InChIKey 
BDYGAPLPLXNVSE-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
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)