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MolNFT v1 · #82709 · protein

Crystal structure of beta secetase in complex with 2-amino-3-methyl-6- ((1S, 2R)-2-PHENYLCYCLOPROPYL)PYRIMIDIN-4(3H)-one

3VV6 · Beta-secretase 1: “Crystal structure of beta secetase in complex with 2-amino-3-methyl-6- ((1S…”. X-ray diffraction, 2 ligands (B00, IOD), 1 pocket (best druggability 0.67). MolNFT v1 #82709 on GenesisL1: 3D structure, binding sites…

PDB
3VV6
Type
protein
Length
360 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
B00, IOD
Pockets
1 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 16% helix, 41% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ABeta-secretase 1 (EC 3.4.23.46)protein36016% helix, 41% strandP56817

Ligands and binding sites

  • B00 · 2-amino-3-methyl-6-[(1S,2R)-2-phenylcyclopropyl]pyrimidin-4(3H)-one · ligand · chains A
  • IOD · Iodide ion · ion · 5 copies · chains A
  • GOL · Glycerol · additive · 4 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
15150.670.7852GOL, B00

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

  • 3VV6 · Crystal Structure of beta secetase in complex with 2-amino-3-methyl-6-((1S… · 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

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