Ligand profile

2SZ

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

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

Via homolog PDB 4okg UniProt P47205 Formula C₃₂H₂₉N₇O₂
Mol. weight 543.63 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2SZ
PDB
4okg
UniProt (similar protein)
P47205
Target protein
VK055_2471

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 543.63 Da
LogP (Crippen) 3.75
H-bond donors 2
H-bond acceptors 8
TPSA 99.41 Ų
Rotatable bonds 5
Aromatic rings 5 / 6
Heavy atoms 41
Fraction sp³ C 0.19
Formula C₃₂H₂₉N₇O₂

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 99.4
  • −1 ≤ LogP ≤ 5 3.75
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 543.6
  • LogP ≤ 5 3.75
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 99.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN1CCN(CC1)Cc2ccc(cn2)C#Cc3ccc(cc3)c4cc(cnc4n5cnc6c5cccc6)C(=O)NO
InChI 
InChI=1S/C32H29N7O2/c1-37-14-16-38(17-15-37)21-27-13-10-24(19-33-27)7-6-23-8-11-25(12-9-23)28-18-26(32(40)36-41)20-34-31(28)39-22-35-29-4-2-3-5-30(29)39/h2-5,8-13,18-20,22,41H,14-17,21H2,1H3,(H,36,40)
InChIKey 
YJCPLYNHCKYCMY-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)