Ligand profile

LZR

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 2w0v UniProt P43889 Formula C₂₅H₂₆N₄O₄
Mol. weight 446.51 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
LZR
PDB
2w0v
UniProt (similar protein)
P43889
Target protein
VK055_3340

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 446.51 Da
LogP (Crippen) 2.63
H-bond donors 1
H-bond acceptors 7
TPSA 89.45 Ų
Rotatable bonds 7
Aromatic rings 3 / 6
Heavy atoms 33
Fraction sp³ C 0.40
Formula C₂₅H₂₆N₄O₄

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 89.4
  • −1 ≤ LogP ≤ 5 2.63
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 446.5
  • LogP ≤ 5 2.63
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 89.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1cc2c(cc1OCC3C=C3)C(=O)NC(=N2)N4CCC5=C(C4)C=CN(C5=O)CC6CC6
InChI 
InChI=1S/C25H26N4O4/c1-32-21-11-20-19(10-22(21)33-14-16-4-5-16)23(30)27-25(26-20)29-9-7-18-17(13-29)6-8-28(24(18)31)12-15-2-3-15/h4-6,8,10-11,15-16H,2-3,7,9,12-14H2,1H3,(H,26,27,30)
InChIKey 
BVRCGDWCYYETOO-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)