Ligand profile

LIP

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

Bound to: VK055_5036 — glycosyl transferases group 1 family protein

Via homolog PDB 3c4v UniProt Q8NTA6 Formula C₆H₁₁O₉P²⁻
Mol. weight 258.12 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
LIP
PDB
3c4v
UniProt (similar protein)
Q8NTA6
Target protein
VK055_5036

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 258.12 Da
LogP (Crippen) -4.98
H-bond donors 5
H-bond acceptors 9
TPSA 173.57 Ų
Rotatable bonds 2
Aromatic rings 0 / 1
Heavy atoms 16
Fraction sp³ C 1.00
Formula C₆H₁₁O₉P²⁻

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 173.6
  • −1 ≤ LogP ≤ 5 -4.98
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 258.1
  • LogP ≤ 5 -4.98
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 173.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[C@H]1([C@@H](C([C@H]([C@@H](C1O)O)O)OP(=O)([O-])[O-])O)O
InChI 
InChI=1S/C6H13O9P/c7-1-2(8)4(10)6(5(11)3(1)9)15-16(12,13)14/h1-11H,(H2,12,13,14)/p-2/t1?,2-,3+,4-,5-,6?/m0/s1
InChIKey 
INAPMGSXUVUWAF-LXOASSSBSA-L

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
PF00534' 'PF13579

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_5036.

PDB 3

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)