Ligand profile

8Q8

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

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

Via homolog PDB 5n8c UniProt P47205 Formula C₂₇H₃₁N₅O₃
Mol. weight 473.58 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
8Q8
PDB
5n8c
UniProt (similar protein)
P47205
Target protein
VK055_2471

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 473.58 Da
LogP (Crippen) 2.01
H-bond donors 5
H-bond acceptors 7
TPSA 125.43 Ų
Rotatable bonds 7
Aromatic rings 3 / 4
Heavy atoms 35
Fraction sp³ C 0.33
Formula C₂₇H₃₁N₅O₃

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 125.4
  • −1 ≤ LogP ≤ 5 2.01
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 473.6
  • LogP ≤ 5 2.01
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 125.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(C(C(=O)NO)NC1CCc2c1ccc(c2)C#Cc3ccc(cc3)Cn4ccnc4CO)N
InChI 
InChI=1S/C27H31N5O3/c1-27(2,28)25(26(34)31-35)30-23-12-10-21-15-19(9-11-22(21)23)6-3-18-4-7-20(8-5-18)16-32-14-13-29-24(32)17-33/h4-5,7-9,11,13-15,23,25,30,33,35H,10,12,16-17,28H2,1-2H3,(H,31,34)
InChIKey 
HMFUASPGNDZNJF-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)