Ligand profile

3SY

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

Bound to: VK055_0067 — aspartate--tRNA ligase

Via homolog PDB 4rmf UniProt A0QWN3 Formula C₅H₁₂O₄
Mol. weight 136.15 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3SY
PDB
4rmf
UniProt (similar protein)
A0QWN3
Target protein
VK055_0067

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 136.15 Da
LogP (Crippen) -2.06
H-bond donors 4
H-bond acceptors 4
TPSA 80.92 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 9
Fraction sp³ C 1.00
Formula C₅H₁₂O₄

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 80.9
  • −1 ≤ LogP ≤ 5 -2.06
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 136.1
  • LogP ≤ 5 -2.06
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 80.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(C(CO)(CO)CO)O
InChI 
InChI=1S/C5H12O4/c6-1-5(2-7,3-8)4-9/h6-9H,1-4H2
InChIKey 
WXZMFSXDPGVJKK-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
PF00152

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_0067.

PDB 2

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 2

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)