MolNFT v1 · #179302 · protein
Crystal structure of human insulin degrading enzyme (ide) in complex with compound BDM_77291
7K1D · Insulin-degrading enzyme: “Crystal structure of human insulin degrading enzyme (ide) in complex with compound BDM_77291”. X-ray diffraction, 2 ligands (VQD, ZN), 20 pockets (best druggability 0.84). MolNFT v1 #179302 on GenesisL1…
- PDB
- 7K1D
- 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
- VQD, ZN
- Pockets
- 20 · best druggability 0.84
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 | 957 | 45% helix, 20% strand | P14735 |
| B | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 958 | 44% helix, 20% strand | P14735 |
Ligands and binding sites
- VQD · (3R)-3-{4-[(3R)-4-(3,4-difluorobenzene-1-carbonyl) morpholin-3-yl]-1H-1,2,3-triazol-1-yl}-N-hydroxy-4-(naphthalen-2-yl)butanamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- DIO · 1,4-diethylene dioxide · additive · 6 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.84 | 0.85 | 100 | empty |
| 2 | 950 | 0.78 | 0.80 | 113 | VQD, DIO |
| 3 | 925 | 0.75 | 0.78 | 105 | VQD, DIO, EPE |
| 4 | 452 | 0.70 | 0.81 | 64 | empty |
| 5 | 504 | 0.66 | 0.78 | 71 | EPE |
Interfaces
1 interface between chains.
- A–B · 1482 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7K1D · Crystal structure of human insulin degrading enzyme (IDE) in complex with compound… · 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 7K1D · PDBe 7K1D · UniProt P14735
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