Ligand profile

2M8

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

Bound to: VK055_1757 — pyridoxal phosphate (PLP) phosphatase

Via homolog PDB 3zx5 UniProt Q72K29 Formula C₉H₁₆O₉
Mol. weight 268.22 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2M8
PDB
3zx5
UniProt (similar protein)
Q72K29
Target protein
VK055_1757

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 268.22 Da
LogP (Crippen) -3.75
H-bond donors 6
H-bond acceptors 8
TPSA 156.91 Ų
Rotatable bonds 5
Aromatic rings 0 / 1
Heavy atoms 18
Fraction sp³ C 0.89
Formula C₉H₁₆O₉

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 156.9
  • −1 ≤ LogP ≤ 5 -3.75
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 268.2
  • LogP ≤ 5 -3.75
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 156.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)O[C@H](CO)C(=O)O)O)O)O)O
InChI 
InChI=1S/C9H16O9/c10-1-3-5(12)6(13)7(14)9(17-3)18-4(2-11)8(15)16/h3-7,9-14H,1-2H2,(H,15,16)/t3-,4-,5-,6+,7+,9-/m1/s1
InChIKey 
DDXCFDOPXBPUJC-SAYMMRJXSA-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
PF08282

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_1757.

PDB 7

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)