Research workbench
Structure of the wnt deacylase notum in complex with isoquinoline 45
Analyse Structure of the wnt deacylase notum in complex with isoquinoline 45 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R8R
- Type
- protein
- Length
- 362 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Palmitoleoyl-protein carboxylesterase notum
- EC
- 3.1.1.98
- UniProt
- Q6P988
- Ligands
- JV8, NAG, SO4
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Palmitoleoyl-protein carboxylesterase notum (EC 3.1.1.98) | protein | 362 | 32% helix, 18% strand | Q6P988 |
Ligands and binding sites
- JV8 · ~{N}-isoquinolin-6-yl-2-(2-methylphenoxy)ethanamide · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · 8 copies · chains A
- EDO · 1,2-ethanediol · additive · 10 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.66 | 0.83 | 32 | JV8, SO4 |
| 2 | 74 | 0.34 | 0.76 | 25 | SO4 |
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6R8R · Structure of the Wnt deacylase Notum in complex with isoquinoline 45 · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q6P988
- Elsewhere: RCSB PDB 6R8R · PDBe 6R8R · UniProt Q6P988
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