Research workbench
Human bace-1 in complex with 7-ethyl-N-((1S,2R)-2-hydroxy-1- (phenylmethyl)-3-(((3-(TRIFLUOROMETHYL)PHENYL)METHYL)AMINO)PROPYL)-1- methyl-3,4-dihydro-1H-(1,2,5)THIADIAZEPINO(3,4,5-HI)INDOLE-9- carboxamide 2,2-dioxide
Analyse Human bace-1 in complex with 7-ethyl-N-((1S,2R)-2-hydroxy-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VNN
- Type
- protein
- Length
- 374 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- CM7
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 374 | 14% helix, 43% strand | P56817 |
Ligands and binding sites
- CM7 · N-[(1S,2R)-1-benzyl-2-hydroxy-3-{[3-(trifluoromethyl)benzyl]amino}propyl]-7-ethyl-1-methyl-3,4-dihydro-1H-[1,2,5]thiadiazepino[3,4,5-hi]indole-9-carboxamide 2,2-dioxide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.67 | 0.81 | 42 | CM7 |
| 2 | 102 | 0.48 | 0.81 | 30 | empty |
| 3 | 111 | 0.44 | 0.78 | 25 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2VNN · Human BACE-1 in complex with 7-ethyl-N-((1S,2R)-2-hydroxy-1-(phenylmethyl)-3-(((3-(trifluo… · the same entry in another collection · chain A against A, TM-score 1.00
- P56817 · AlphaFold monomer V2.0 prediction for beta-secretase 1 (P56817) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P56817
- Elsewhere: RCSB PDB 2VNN · PDBe 2VNN · UniProt P56817
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