Ligand profile

DSD

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

Bound to: VK055_1728 — dethiobiotin synthase

Via homolog PDB 1daf UniProt P13000 Formula C₁₀H₂₀N₂O₄
Mol. weight 232.28 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DSD
PDB
1daf
UniProt (similar protein)
P13000
Target protein
VK055_1728

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 232.28 Da
LogP (Crippen) 1.00
H-bond donors 4
H-bond acceptors 3
TPSA 112.65 Ų
Rotatable bonds 8
Aromatic rings 0 / 0
Heavy atoms 16
Fraction sp³ C 0.80
Formula C₁₀H₂₀N₂O₄

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 112.7
  • −1 ≤ LogP ≤ 5 1.00
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 232.3
  • LogP ≤ 5 1.00
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 112.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]([C@@H](CCCCCC(=O)O)NC(=O)O)N
InChI 
InChI=1S/C10H20N2O4/c1-7(11)8(12-10(15)16)5-3-2-4-6-9(13)14/h7-8,12H,2-6,11H2,1H3,(H,13,14)(H,15,16)/t7-,8+/m0/s1
InChIKey 
OQNJZSIPDMTUAJ-JGVFFNPUSA-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
PF01656

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_1728.

PDB 8

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)