Ligand profile

1JS

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

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

Via homolog PDB 4j3d UniProt P47205 Formula C₂₃H₂₅N₃O₅
Mol. weight 423.47 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1JS
PDB
4j3d
UniProt (similar protein)
P47205
Target protein
VK055_2471

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 423.47 Da
LogP (Crippen) 0.97
H-bond donors 5
H-bond acceptors 5
TPSA 127.76 Ų
Rotatable bonds 9
Aromatic rings 2 / 2
Heavy atoms 31
Fraction sp³ C 0.26
Formula C₂₃H₂₅N₃O₅

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 127.8
  • −1 ≤ LogP ≤ 5 0.97
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 423.5
  • LogP ≤ 5 0.97
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 127.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)C#Cc2ccc(cc2)C(=O)NC(CCC(=O)NCCCO)C(=O)NO
InChI 
InChI=1S/C23H25N3O5/c27-16-4-15-24-21(28)14-13-20(23(30)26-31)25-22(29)19-11-9-18(10-12-19)8-7-17-5-2-1-3-6-17/h1-3,5-6,9-12,20,27,31H,4,13-16H2,(H,24,28)(H,25,29)(H,26,30)
InChIKey 
CNHUGIBXGNVURP-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
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)