Ligand profile

B3P

Ligand co-crystallized with this exact protein (Protein Data Bank).

Bound to: VK055_1755 — 6-phosphogluconolactonase

Direct evidence PDB 6nau UniProt A6T6J6 Formula C₁₁H₂₆N₂O₆
Mol. weight 282.34 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
B3P
PDB
6nau
UniProt (this protein)
A6T6J6
Target protein
VK055_1755

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 282.34 Da
LogP (Crippen) -4.01
H-bond donors 8
H-bond acceptors 8
TPSA 145.44 Ų
Rotatable bonds 12
Aromatic rings 0 / 0
Heavy atoms 19
Fraction sp³ C 1.00
Formula C₁₁H₂₆N₂O₆

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 145.4
  • −1 ≤ LogP ≤ 5 -4.01
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 282.3
  • LogP ≤ 5 -4.01
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 145.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CNC(CO)(CO)CO)CNC(CO)(CO)CO
InChI 
InChI=1S/C11H26N2O6/c14-4-10(5-15,6-16)12-2-1-3-13-11(7-17,8-18)9-19/h12-19H,1-9H2
InChIKey 
HHKZCCWKTZRCCL-UHFFFAOYSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF10282

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_1755.

ZINC 9

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

Compound Similarity (Tanimoto)