Ligand profile

1SF

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

Bound to: VK055_3340 — UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase

Via homolog PDB 4kpz UniProt P43889 Formula C₁₀H₉N₃O₄
Mol. weight 235.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1SF
PDB
4kpz
UniProt (similar protein)
P43889
Target protein
VK055_3340

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 235.20 Da
LogP (Crippen) 1.04
H-bond donors 1
H-bond acceptors 4
TPSA 92.55 Ų
Rotatable bonds 2
Aromatic rings 1 / 2
Heavy atoms 17
Fraction sp³ C 0.20
Formula C₁₀H₉N₃O₄

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 92.6
  • −1 ≤ LogP ≤ 5 1.04
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 235.2
  • LogP ≤ 5 1.04
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 92.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(cc(c1)[N+](=O)[O-])N2CCC(=O)NC2=O
InChI 
InChI=1S/C10H9N3O4/c14-9-4-5-12(10(15)11-9)7-2-1-3-8(6-7)13(16)17/h1-3,6H,4-5H2,(H,11,14,15)
InChIKey 
GMUGBPYYXAGNCT-UHFFFAOYSA-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
PF12804

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_3340.

PDB 11

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

Ligand PDB entry

ChEMBL 35

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)