Ligand profile

1S9

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 4knx UniProt P43889 Formula C₂₄H₂₀N₄O₅
Mol. weight 444.45 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1S9
PDB
4knx
UniProt (similar protein)
P43889
Target protein
VK055_3340

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 444.45 Da
LogP (Crippen) 4.10
H-bond donors 3
H-bond acceptors 7
TPSA 122.67 Ų
Rotatable bonds 8
Aromatic rings 4 / 4
Heavy atoms 33
Fraction sp³ C 0.08
Formula C₂₄H₂₀N₄O₅

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 122.7
  • −1 ≤ LogP ≤ 5 4.10
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 444.4
  • LogP ≤ 5 4.10
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 122.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1cc2c(cc1OCC(=O)O)ncnc2Nc3ccc(cc3)NC(=O)c4ccccc4
InChI 
InChI=1S/C24H20N4O5/c1-32-20-11-18-19(12-21(20)33-13-22(29)30)25-14-26-23(18)27-16-7-9-17(10-8-16)28-24(31)15-5-3-2-4-6-15/h2-12,14H,13H2,1H3,(H,28,31)(H,29,30)(H,25,26,27)
InChIKey 
VAJKCEBFUQHYLC-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)