MolNFT v1 · #55612 · protein
Human insulin degrading enzyme E111Q in complex with inhibitor compound 41367
2YPU · Insulin-degrading enzyme: “Human insulin degrading enzyme E111Q in complex with inhibitor compound 41367”. X-ray diffraction, 2 ligands (I41, ZN), 20 pockets (best druggability 0.85). MolNFT v1 #55612 on GenesisL1: 3D structure…
- PDB
- 2YPU
- Type
- protein
- Length
- 1,910 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin-degrading enzyme
- EC
- 3.4.24.56
- UniProt
- P14735
- Ligands
- I41, ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 956 | 44% helix, 20% strand | P14735 |
| B | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 954 | 45% helix, 20% strand | P14735 |
Ligands and binding sites
- I41 · 2-[[2-[[(2S)-3-(3H-imidazol-4-yl)-1-methoxy-1-oxo-propan-2-yl]amino]-2-oxo-ethyl]-(phenylmethyl)amino]ethanoic acid · 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.85 | 0.86 | 99 | empty |
| 2 | 845 | 0.75 | 0.79 | 117 | ZN |
| 3 | 712 | 0.72 | 0.79 | 95 | empty |
| 4 | 508 | 0.70 | 0.80 | 72 | empty |
| 5 | 350 | 0.66 | 0.81 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 1578 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2YPU · human insulin degrading enzyme E111Q in complex with inhibitor compound 41367 · 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 2YPU · PDBe 2YPU · UniProt P14735
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