Ligand profile

MZR

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

Bound to: VK055_2780 — pfkB carbohydrate kinase family protein

Via homolog PDB 3b1n UniProt Q2SZE4 Formula C₉H₁₃N₃O₆
Mol. weight 259.22 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
MZR
PDB
3b1n
UniProt (similar protein)
Q2SZE4
Target protein
VK055_2780

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 259.22 Da
LogP (Crippen) -2.70
H-bond donors 5
H-bond acceptors 8
TPSA 151.06 Ų
Rotatable bonds 3
Aromatic rings 1 / 2
Heavy atoms 18
Fraction sp³ C 0.56
Formula C₉H₁₃N₃O₆

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 151.1
  • −1 ≤ LogP ≤ 5 -2.70
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 259.2
  • LogP ≤ 5 -2.70
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 151.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c(n1[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O)O)C(=O)N
InChI 
InChI=1S/C9H13N3O6/c10-7(16)4-8(17)12(2-11-4)9-6(15)5(14)3(1-13)18-9/h2-3,5-6,9,13-15,17H,1H2,(H2,10,16)/t3-,5-,6-,9-/m1/s1
InChIKey 
HZQDCMWJEBCWBR-UUOKFMHZSA-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
PF00294

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_2780.

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)