Ligand profile

DS0

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

Bound to: VK055_2233 — D-alanine-D-alanine ligase A

Via homolog PDB 6u1i UniProt Q5SHZ3 Formula C₃H₇N₂O₅P
Mol. weight 182.07 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DS0
PDB
6u1i
UniProt (similar protein)
Q5SHZ3
Target protein
VK055_2233

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 182.07 Da
LogP (Crippen) -1.23
H-bond donors 3
H-bond acceptors 5
TPSA 114.37 Ų
Rotatable bonds 1
Aromatic rings 0 / 1
Heavy atoms 11
Fraction sp³ C 0.67
Formula C₃H₇N₂O₅P

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 114.4
  • −1 ≤ LogP ≤ 5 -1.23
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 182.1
  • LogP ≤ 5 -1.23
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 114.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@H](C(=NO1)OP(=O)(O)O)N
InChI 
InChI=1S/C3H7N2O5P/c4-2-1-9-5-3(2)10-11(6,7)8/h2H,1,4H2,(H2,6,7,8)/t2-/m1/s1
InChIKey 
SFMNESRSKJTEMJ-UWTATZPHSA-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
PF01820' 'PF07478

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_2233.

PDB 3

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)