Research workbench
Crystal structure of insulin degrading enzyme complexed with inhibitor tert-butyl [(2S)-2-(2,5-difluorophenyl)-3-(quinolin-3-yl) PROPYL]CARBAMATE
Analyse Crystal structure of insulin degrading enzyme complexed with inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PES
- Type
- protein
- Length
- 1,920 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin-degrading enzyme; Ala-ala-ala
- EC
- 3.4.24.56
- UniProt
- P14735
- Ligands
- 2PJ, ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 955 | 44% helix, 20% strand | P14735 |
| B | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 959 | 44% helix, 20% strand | P14735 |
| C, D | Ala-ala-ala | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- 2PJ · tert-butyl [(2S)-2-(2,5-difluorophenyl)-3-(quinolin-3-yl)propyl]carbamate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.86 | 0.87 | 122 | empty |
| 2 | 918 | 0.79 | 0.81 | 115 | empty |
| 3 | 601 | 0.74 | 0.81 | 52 | empty |
| 4 | 604 | 0.74 | 0.81 | 50 | empty |
| 5 | 509 | 0.69 | 0.79 | 56 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1421 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 209 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 206 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4PES · Crystal structure of insulin degrading enzyme complexed with inhibitor tert-butyl… · 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 P14735
- Elsewhere: RCSB PDB 4PES · PDBe 4PES · UniProt P14735
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