Ligand profile

ZINC12405025

Virtual-screening candidate from ZINC.

Bound to: VK055_1757 — pyridoxal phosphate (PLP) phosphatase

Via homolog UniProt Q72K29 Formula C₁₂H₂₂O₁₂
Tanimoto 0.61
Mol. weight 358.30 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC12405025
UniProt (similar protein)
Q72K29
Tanimoto
0.610
Target protein
VK055_1757

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 358.30 Da
LogP (Crippen) -5.67
H-bond donors 9
H-bond acceptors 11
TPSA 217.60 Ų
Rotatable bonds 8
Aromatic rings 0 / 1
Heavy atoms 24
Fraction sp³ C 0.92
Formula C₁₂H₂₂O₁₂

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 217.6
  • −1 ≤ LogP ≤ 5 -5.67
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 358.3
  • LogP ≤ 5 -5.67
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 217.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(O)[C@H](O)[C@H](O)[C@H](O[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O)[C@@H](O)CO
InChI 
InChI=1S/C12H22O12/c13-1-3(15)10(7(18)8(19)11(21)22)24-12-9(20)6(17)5(16)4(2-14)23-12/h3-10,12-20H,1-2H2,(H,21,22)/t3-,4+,5-,6-,7-,8+,9+,10+,12-/m0/s1
InChIKey 
JYTUSYBCFIZPBE-WJVZIYFOSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
2M8
Homolog
Q72K29

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 8

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)