Ligand profile

7TD

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

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

Via homolog PDB 5u3b UniProt P47205 Formula C₁₆H₂₁N₃O₄
Mol. weight 319.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
7TD
PDB
5u3b
UniProt (similar protein)
P47205
Target protein
VK055_2471

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 319.36 Da
LogP (Crippen) 0.43
H-bond donors 4
H-bond acceptors 5
TPSA 113.68 Ų
Rotatable bonds 6
Aromatic rings 1 / 1
Heavy atoms 23
Fraction sp³ C 0.38
Formula C₁₆H₂₁N₃O₄

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 113.7
  • −1 ≤ LogP ≤ 5 0.43
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 319.4
  • LogP ≤ 5 0.43
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 113.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC#CCOc1ccc(cc1)C(=O)NC(C(=O)NO)C(C)(C)N
InChI 
InChI=1S/C16H21N3O4/c1-4-5-10-23-12-8-6-11(7-9-12)14(20)18-13(15(21)19-22)16(2,3)17/h6-9,13,22H,10,17H2,1-3H3,(H,18,20)(H,19,21)
InChIKey 
JPCUWLVKAJJSLN-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)