MolNFT v1 · #144614 · protein
Structure of cysteine-free human insulin-degrading enzyme in complex with substrate-selective macrocyclic inhibitor 37
6BYZ: “Structure of cysteine-free human insulin-degrading enzyme in complex with substrate-selective macrocyclic…”. X-ray diffraction, 1 ligand (J18), 20 pockets (best druggability 0.79). MolNFT v1 #144614 on GenesisL1: 3D structure…
- PDB
- 6BYZ
- Type
- protein
- Length
- 1,923 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
- J18
- Pockets
- 20 · best druggability 0.79
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 | 959 | 44% helix, 20% strand | P14735 |
| B | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 958 | 44% helix, 20% strand | P14735 |
| D, E | Ala-ala-ala | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- J18 · [(8R,9S,10S)-9-(2',3'-dimethyl[1,1'-biphenyl]-4-yl)-6-{[2-(trifluoromethyl)phenyl]sulfonyl}-1,6-diazabicyclo[6.2.0]decan-10-yl]methanol · ligand · 2 copies · chains A, D, B, E
- 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.79 | 0.80 | 100 | empty |
| 2 | 960 | 0.75 | 0.78 | 106 | J18 |
| 3 | 591 | 0.71 | 0.79 | 95 | empty |
| 4 | 404 | 0.69 | 0.81 | 41 | empty |
| 5 | 549 | 0.68 | 0.78 | 70 | EPE |
Interfaces
3 interfaces between chains.
- A–B · 894 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 201 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 200 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6BYZ · Structure of Cysteine-free Human Insulin-Degrading Enzyme in complex with… · 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 6BYZ · PDBe 6BYZ · UniProt P14735
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