MolNFT v1 · #124814 · protein
(4~{S},6~{S})-4-[2,4-BIS(FLUORANYL)PHENYL]-4-methyl-6-pyrimidin-5-yl- 5,6-dihydro-1,3-thiazin-2-amine (compound 12) bound to BACE1
5KQF · Beta-secretase 1: “(4~{S},6~{S})-4-[2,4-BIS(FLUORANYL)PHENYL]-4-methyl-6-pyrimidin-5-yl- 5,6-dihydro-1,3-thiazin-2-amine…”. X-ray diffraction, 1 ligand (6WD), 2 pockets (best druggability 0.62). MolNFT v1 #124814 on GenesisL1: 3D…
- PDB
- 5KQF
- Type
- protein
- Length
- 358 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
- 6WD
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 358 | 16% helix, 41% strand | P56817 |
Ligands and binding sites
- 6WD · (4~{S},6~{S})-4-[2,4-bis(fluoranyl)phenyl]-4-methyl-6-pyrimidin-5-yl-5,6-dihydro-1,3-thiazin-2-amine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.62 | 0.77 | 50 | 6WD |
| 2 | 54 | 0.29 | 0.75 | 13 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5KQF · (4~{S},6~{S})-4-[2,4-bis(fluoranyl)phenyl]-4-methyl-6-pyrimidin-5-yl-5,6-dihydro-1,3-thiaz… · 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 0.99
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 5KQF · PDBe 5KQF · UniProt P56817
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