Ligand profile

C90

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

Bound to: VK055_2471 — UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosaminedeacetylase

Via homolog PDB 3nzk UniProt A1JJJ9 Formula C₂₄H₂₇N₃O₅
Mol. weight 437.50 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
C90
PDB
3nzk
UniProt (similar protein)
A1JJJ9
Target protein
VK055_2471

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 437.50 Da
LogP (Crippen) 0.90
H-bond donors 4
H-bond acceptors 6
TPSA 111.13 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 32
Fraction sp³ C 0.33
Formula C₂₄H₂₇N₃O₅

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 111.1
  • −1 ≤ LogP ≤ 5 0.90
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 437.5
  • LogP ≤ 5 0.90
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 111.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C(C(=O)NO)NC(=O)c1ccc(cc1)C#Cc2ccc(cc2)CN3CCOCC3)O
InChI 
InChI=1S/C24H27N3O5/c1-17(28)22(24(30)26-31)25-23(29)21-10-8-19(9-11-21)3-2-18-4-6-20(7-5-18)16-27-12-14-32-15-13-27/h4-11,17,22,28,31H,12-16H2,1H3,(H,25,29)(H,26,30)
InChIKey 
FQYBTYFKOHPWQT-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF03331

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_2471.

PDB 40

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

Ligand PDB entry

ChEMBL 100

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)