MolNFT v1 · #85788 · protein
Prolyl oligopeptidase from porcine brain with a covalently bound inhibitor ic-2
4AMZ · Prolyl endopeptidase: “Prolyl oligopeptidase from porcine brain with a covalently bound inhibitor ic-2”. X-ray diffraction, 1 ligand (2P4), 9 pockets (best druggability 0.73). MolNFT v1 #85788 on GenesisL1: 3D structure, binding…
- PDB
- 4AMZ
- 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
- 2P4
- Pockets
- 9 · 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
- 2P4 · (5R)-N-benzyl-5-({(2S)-2-[(1R)-1,2-dihydroxyethyl]pyrrolidin-1-yl}carbonyl)cyclopent-1-ene-1-carboxamide · ligand · chains A
- GOL · Glycerol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.73 | 0.79 | 69 | empty |
| 2 | 466 | 0.66 | 0.78 | 44 | GOL |
| 3 | 266 | 0.55 | 0.77 | 34 | 2P4 |
| 4 | 95 | 0.50 | 0.82 | 25 | empty |
| 5 | 106 | 0.41 | 0.76 | 17 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4AMZ · Prolyl oligopeptidase from porcine brain with a covalently bound inhibitor ic-2 · 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 4AMZ · PDBe 4AMZ · UniProt P23687
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