Ligand profile

M2P

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

Bound to: VK055_3965 — deoC/LacD aldolase family protein

Via homolog PDB 2yce UniProt P58315 Formula C₆H₁₆O₁₂P₂
Mol. weight 342.13 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
M2P
PDB
2yce
UniProt (similar protein)
P58315
Target protein
VK055_3965

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 342.13 Da
LogP (Crippen) -3.35
H-bond donors 8
H-bond acceptors 8
TPSA 214.44 Ų
Rotatable bonds 9
Aromatic rings 0 / 0
Heavy atoms 20
Fraction sp³ C 1.00
Formula C₆H₁₆O₁₂P₂

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 214.4
  • −1 ≤ LogP ≤ 5 -3.35
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 342.1
  • LogP ≤ 5 -3.35
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 214.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@H]([C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)O)OP(=O)(O)O
InChI 
InChI=1S/C6H16O12P2/c7-3(1-17-19(11,12)13)5(9)6(10)4(8)2-18-20(14,15)16/h3-10H,1-2H2,(H2,11,12,13)(H2,14,15,16)/t3-,4-,5-,6-/m1/s1
InChIKey 
WOYYTQHMNDWRCW-KVTDHHQDSA-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
PF01791

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_3965.

PDB 5

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)