Ligand profile

F64

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

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

Via homolog PDB 6c9c UniProt Q02H34 Formula C₂₄H₂₈ClN₃O₇S
Mol. weight 538.02 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
F64
PDB
6c9c
UniProt (similar protein)
Q02H34
Target protein
VK055_2471

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 538.02 Da
LogP (Crippen) 2.64
H-bond donors 2
H-bond acceptors 8
TPSA 135.13 Ų
Rotatable bonds 10
Aromatic rings 2 / 3
Heavy atoms 36
Fraction sp³ C 0.38
Formula C₂₄H₂₈ClN₃O₇S

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 135.1
  • −1 ≤ LogP ≤ 5 2.64
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 538.0
  • LogP ≤ 5 2.64
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 135.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@](CCN1CC=C(CC1=O)c2ccc(cc2)OCc3cc(c(nc3)OC)Cl)(C(=O)NO)S(=O)(=O)C
InChI 
InChI=1S/C24H28ClN3O7S/c1-24(23(30)27-31,36(3,32)33)9-11-28-10-8-18(13-21(28)29)17-4-6-19(7-5-17)35-15-16-12-20(25)22(34-2)26-14-16/h4-8,12,14,31H,9-11,13,15H2,1-3H3,(H,27,30)/t24-/m0/s1
InChIKey 
CDFIGPHKVBKXMP-DEOSSOPVSA-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)