MolNFT v1 · #103387 · protein
Crystal structure of insulin degrading enzyme complexed with inhibitor
4PF9 · Insulin-degrading enzyme: “Crystal structure of insulin degrading enzyme complexed with inhibitor”. X-ray diffraction, 2 ligands (2Q6, ZN), 20 pockets (best druggability 0.83). MolNFT v1 #103387 on GenesisL1: 3D structure, binding…
- PDB
- 4PF9
- Type
- protein
- Length
- 1,915 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
- 2Q6, ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 959 | 43% helix, 20% strand | P14735 |
| B | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 956 | 43% helix, 20% strand | P14735 |
Ligands and binding sites
- 2Q6 · methyl [(2S)-2-[4-({5-[4-({(2S)-2-[(3S)-3-amino-2-oxopiperidin-1-yl]-2-cyclohexylacetyl}amino)phenyl]pentyl}oxy)phenyl]-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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.83 | 0.84 | 117 | empty |
| 2 | 950 | 0.75 | 0.78 | 107 | 2Q6 |
| 3 | 1000 | 0.74 | 0.77 | 82 | empty |
| 4 | 838 | 0.71 | 0.76 | 78 | empty |
| 5 | 335 | 0.71 | 0.84 | 51 | empty |
Interfaces
1 interface between chains.
- A–B · 1564 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4PF9 · Crystal structure of insulin degrading enzyme complexed with inhibitor · 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 4PF9 · PDBe 4PF9 · UniProt P14735
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