Ligand profile

1SE

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 4kpx UniProt P43889 Formula C₁₉H₁₄N₄O₅
Mol. weight 378.34 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1SE
PDB
4kpx
UniProt (similar protein)
P43889
Target protein
VK055_3340

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 378.34 Da
LogP (Crippen) 3.20
H-bond donors 3
H-bond acceptors 6
TPSA 134.46 Ų
Rotatable bonds 5
Aromatic rings 3 / 3
Heavy atoms 28
Fraction sp³ C 0.00
Formula C₁₉H₁₄N₄O₅

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 134.5
  • −1 ≤ LogP ≤ 5 3.20
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 378.3
  • LogP ≤ 5 3.20
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 134.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccnc(c1)C(=O)Nc2ccc(cc2)NC(=O)c3ccc(c(c3)[N+](=O)[O-])O
InChI 
InChI=1S/C19H14N4O5/c24-17-9-4-12(11-16(17)23(27)28)18(25)21-13-5-7-14(8-6-13)22-19(26)15-3-1-2-10-20-15/h1-11,24H,(H,21,25)(H,22,26)
InChIKey 
QFXQBOSIGGGQEW-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)