Ligand profile

LY9

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

Bound to: VK055_4987 — isomerase/lactonizing enzyme

Via homolog PDB 3ozm UniProt A0A0H3LT39 Formula C₅H₈O₇
Mol. weight 180.11 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
LY9
PDB
3ozm
UniProt (similar protein)
A0A0H3LT39
Target protein
VK055_4987

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 180.11 Da
LogP (Crippen) -2.76
H-bond donors 5
H-bond acceptors 5
TPSA 135.29 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 12
Fraction sp³ C 0.60
Formula C₅H₈O₇

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 135.3
  • −1 ≤ LogP ≤ 5 -2.76
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 180.1
  • LogP ≤ 5 -2.76
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 135.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[C@@H](C([C@H](C(=O)O)O)O)(C(=O)O)O
InChI 
InChI=1S/C5H8O7/c6-1(2(7)4(9)10)3(8)5(11)12/h1-3,6-8H,(H,9,10)(H,11,12)/t2-,3-/m1/s1
InChIKey 
NPTTZSYLTYJCPR-PWNYCUMCSA-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
PF02746' 'PF13378

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_4987.

PDB 9

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)