Ligand profile

NOJ

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

Bound to: VK055_0025 — amylase

Via homolog PDB 1i75 UniProt P05618 Formula C₆H₁₃NO₄
Mol. weight 163.17 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NOJ
PDB
1i75
UniProt (similar protein)
P05618
Target protein
VK055_0025

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 163.17 Da
LogP (Crippen) -2.97
H-bond donors 5
H-bond acceptors 5
TPSA 92.95 Ų
Rotatable bonds 1
Aromatic rings 0 / 1
Heavy atoms 11
Fraction sp³ C 1.00
Formula C₆H₁₃NO₄

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 93.0
  • −1 ≤ LogP ≤ 5 -2.97
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 163.2
  • LogP ≤ 5 -2.97
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 93.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@@H]([C@H]([C@@H]([C@H](N1)CO)O)O)O
InChI 
InChI=1S/C6H13NO4/c8-2-3-5(10)6(11)4(9)1-7-3/h3-11H,1-2H2/t3-,4+,5-,6-/m1/s1
InChIKey 
LXBIFEVIBLOUGU-JGWLITMVSA-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
PF00128' 'PF00686

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_0025.

PDB 2

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

Ligand PDB entry

ZINC 1

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

Compound Similarity (Tanimoto)