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Prolyl oligopeptidase from porcine brain with a covalently bound P2-substituted N-acyl-prolylpyrrolidine inhibitor
Analyse Prolyl oligopeptidase from porcine brain with a covalently bound P2-substituted… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BCC
- Type
- protein
- Length
- 710 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl endopeptidase
- EC
- 3.4.21.26
- UniProt
- P23687
- Ligands
- JKT, TAM
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl endopeptidase (EC 3.4.21.26) | protein | 710 | 23% helix, 33% strand | P23687 |
Ligands and binding sites
- JKT · tert-butyl N-[[1-[(3S,5S)-5-[(2S)-2-[azanyl(oxidanyl)methyl]pyrrolidin-1-yl]carbonyl-1-(4-phenylbutanoyl)pyrrolidin-3-yl]-1,2,3-triazol-4-yl]methyl]carbamate · ligand · chains A
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains A
- GOL · Glycerol · additive · 9 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 736 | 0.73 | 0.79 | 75 | GOL |
| 2 | 459 | 0.66 | 0.78 | 36 | GOL |
| 3 | 289 | 0.56 | 0.76 | 33 | JKT |
| 4 | 101 | 0.52 | 0.83 | 26 | empty |
| 5 | 94 | 0.40 | 0.77 | 17 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4BCC · PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A COVALENTLY BOUND P2- substituted… · the same entry in another collection · chain A against A, TM-score 1.00
- P23687 · AlphaFold monomer V2.0 prediction for prolyl endopeptidase (P23687) · a predicted model of the same protein · 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 P23687
- Elsewhere: RCSB PDB 4BCC · PDBe 4BCC · UniProt P23687
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