Research workbench
Glucopyranosylidene-spiro-iminothiazolidinone, a new bicyclic ring system: synthesis, derivatization, and evaluation as glycogen phosphorylase inhibitors by enzyme kinetic and crystallographic methods
Analyse Glucopyranosylidene-spiro-iminothiazolidinone, a new bicyclic ring system… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CTN
- Type
- protein
- Length
- 807 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen phosphorylase, muscle form
- EC
- 2.4.1.1
- UniProt
- P00489
- Ligands
- M8P, PLP
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen phosphorylase, muscle form (EC 2.4.1.1) | protein | 807 | 54% helix, 15% strand | P00489 |
Ligands and binding sites
- M8P · N-[(2Z,5R,7R,8S,9S,10R)-8,9,10-trihydroxy-7-(hydroxymethyl)-4-oxo-6-oxa-1-thia-3-azaspiro[4.5]dec-2-ylidene]naphthalene-2-carboxamide · ligand · chains A
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 302 | 0.85 | 0.95 | 50 | DMS, M8P, PLP |
| 2 | 91 | 0.72 | 0.94 | 28 | empty |
| 3 | 260 | 0.68 | 0.84 | 35 | empty |
| 4 | 135 | 0.53 | 0.81 | 21 | empty |
| 5 | 211 | 0.49 | 0.76 | 19 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4CTN · Glucopyranosylidene-spiro-iminothiazolidi , a New Bicyclic Ring System: Synthesis… · 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 P00489
- Elsewhere: RCSB PDB 4CTN · PDBe 4CTN · UniProt P00489
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