Research workbench
Crystal structure of insulin degrading enzyme in complex with BDM44768
Analyse Crystal structure of insulin degrading enzyme in complex with BDM44768 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NXO
- Type
- protein
- Length
- 1,914 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
- 2H7, 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 | 958 | 44% helix, 20% strand | P14735 |
| B | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 956 | 45% helix, 21% strand | P14735 |
Ligands and binding sites
- 2H7 · 4-fluoro-N-({1-[(2R)-4-(hydroxyamino)-1-(naphthalen-2-yl)-4-oxobutan-2-yl]-1H-1,2,3-triazol-4-yl}methyl)benzamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
- DIO · 1,4-diethylene dioxide · additive · chains 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 | 1116 | 0.85 | 0.86 | 100 | empty |
| 2 | 904 | 0.76 | 0.79 | 104 | 2H7, PEG, EPE |
| 3 | 875 | 0.75 | 0.79 | 102 | 2H7, PEG, EPE |
| 4 | 239 | 0.65 | 0.83 | 43 | PEG |
| 5 | 297 | 0.64 | 0.80 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 1611 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4NXO · Crystal Structure of Insulin Degrading Enzyme in complex with BDM44768 · 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 4NXO · PDBe 4NXO · UniProt P14735
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