Fluorine in PDB 4wy6: Crystal Structure of Human Bace-1 Bound to Compound 36

All present enzymatic activity of Crystal Structure of Human Bace-1 Bound to Compound 36:
3.4.23.46;

The structure of Crystal Structure of Human Bace-1 Bound to Compound 36, PDB code: 4wy6 was solved by F.F.Vajdos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.41 / 2.10
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	102.871, 102.871, 170.884, 90.00, 90.00, 120.00
R / Rfree (%)	18.5 / 20.1

The structure of Crystal Structure of Human Bace-1 Bound to Compound 36 also contains other interesting chemical elements:

Iodine

(I)

5 atoms

The binding sites of Fluorine atom in the Crystal Structure of Human Bace-1 Bound to Compound 36 (pdb code 4wy6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Human Bace-1 Bound to Compound 36, PDB code: 4wy6:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Human Bace-1 Bound to Compound 36


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human Bace-1 Bound to Compound 36 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:32.6 occ:1.00 F1 A:3VP401 0.0 32.6 1.0 C6 A:3VP401 1.3 33.4 1.0 C5 A:3VP401 2.3 32.4 1.0 C1 A:3VP401 2.4 31.1 1.0 H5 A:3VP401 2.6 32.3 0.0 H3 A:3VP401 2.6 31.0 0.0 H11 A:DMS407 3.2 81.0 1.0 H12 A:DMS407 3.3 81.0 1.0 O A:HOH578 3.4 41.1 1.0 CZ2 A:TRP115 3.4 29.2 1.0 C4 A:3VP401 3.6 32.5 1.0 O A:HOH529 3.6 30.3 1.0 C2 A:3VP401 3.6 30.1 1.0 CH2 A:TRP115 3.6 29.6 1.0 C1 A:DMS407 3.6 81.0 1.0 CD1 A:LEU30 3.9 36.8 1.0 O A:HOH580 4.1 61.9 1.0 S A:DMS407 4.1 82.6 1.0 C3 A:3VP401 4.1 32.7 1.0 CD1 A:ILE110 4.1 36.6 1.0 O A:PHE108 4.3 33.1 1.0 H4 A:3VP401 4.5 30.0 0.0 CE2 A:TRP115 4.5 30.1 1.0 H13 A:DMS407 4.6 81.0 1.0 F2 A:3VP401 4.7 34.6 1.0 CZ3 A:TRP115 4.8 29.1 1.0 CD2 A:LEU30 4.8 36.6 1.0 O A:DMS407 4.9 83.9 1.0 CG1 A:ILE110 4.9 33.6 1.0 CG A:LEU30 4.9 35.0 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Human Bace-1 Bound to Compound 36


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human Bace-1 Bound to Compound 36 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:34.6 occ:1.00 F2 A:3VP401 0.0 34.6 1.0 C4 A:3VP401 1.3 32.5 1.0 C5 A:3VP401 2.3 32.4 1.0 H6 A:3VP401 2.3 34.0 0.0 H2 A:3VP401 2.3 35.8 0.0 C3 A:3VP401 2.4 32.7 1.0 H5 A:3VP401 2.6 32.3 0.0 C7 A:3VP401 2.9 35.3 1.0 C8 A:3VP401 3.0 34.0 1.0 C11 A:3VP401 3.1 35.8 1.0 OH A:TYR71 3.1 38.7 1.0 CZ A:TYR71 3.2 36.2 1.0 CD1 A:PHE108 3.4 35.3 1.0 CE2 A:TYR71 3.5 33.6 1.0 CE1 A:PHE108 3.5 36.6 1.0 C6 A:3VP401 3.6 33.4 1.0 C2 A:3VP401 3.6 30.1 1.0 H1 A:3VP401 3.6 36.3 0.0 CE1 A:TYR71 3.7 32.4 1.0 H11 A:3VP401 3.7 36.8 0.0 H7 A:3VP401 3.7 34.0 0.0 C12 A:3VP401 3.9 36.8 1.0 O A:HOH537 4.0 36.4 1.0 O1 A:3VP401 4.1 36.2 1.0 C1 A:3VP401 4.1 31.1 1.0 C9 A:3VP401 4.1 36.3 1.0 C10 A:3VP401 4.2 32.8 1.0 CD2 A:TYR71 4.3 32.9 1.0 N1 A:3VP401 4.3 37.1 1.0 CD1 A:TYR71 4.4 33.4 1.0 H4 A:3VP401 4.5 30.0 0.0 H10 A:3VP401 4.5 36.8 0.0 F1 A:3VP401 4.7 32.6 1.0 H8 A:3VP401 4.7 32.9 0.0 CG A:PHE108 4.7 33.0 1.0 CG A:TYR71 4.7 32.8 1.0 O A:HOH576 4.8 58.0 1.0 CD1 A:ILE118 4.8 41.8 1.0 CZ A:PHE108 4.8 35.5 1.0 O A:HOH580 4.9 61.9 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Human Bace-1 Bound to Compound 36


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human Bace-1 Bound to Compound 36 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:40.9 occ:1.00 F3 A:3VP401 0.0 40.9 1.0 C14 A:3VP401 1.3 39.3 1.0 H15 A:3VP401 2.0 39.3 0.0 H14 A:3VP401 2.0 39.3 0.0 C9 A:3VP401 2.4 36.3 1.0 H1 A:3VP401 2.6 36.3 0.0 O1 A:3VP401 2.8 36.2 1.0 O A:HOH644 3.1 35.1 1.0 O A:HOH641 3.3 35.5 1.0 CG1 A:VAL69 3.6 33.9 1.0 C10 A:3VP401 3.7 32.8 1.0 O A:HOH705 3.8 41.1 1.0 NH2 A:ARG128 3.9 61.9 1.0 CZ A:ARG128 3.9 68.9 1.0 H8 A:3VP401 4.0 32.9 0.0 H9 A:3VP401 4.0 32.9 0.0 C8 A:3VP401 4.1 34.0 1.0 NE A:ARG128 4.2 53.8 1.0 O A:HOH633 4.2 38.9 1.0 H6 A:3VP401 4.2 34.0 0.0 NH1 A:ARG128 4.3 57.5 1.0 CB A:SER35 4.4 26.3 1.0 O A:HOH571 4.5 58.0 1.0 H7 A:3VP401 4.6 34.0 0.0 O A:HOH550 4.6 61.5 1.0 CB A:TYR71 4.6 33.3 1.0 CD1 A:TYR71 4.8 33.4 1.0 C11 A:3VP401 4.9 35.8 1.0 CG A:TYR71 4.9 32.8 1.0 CD A:ARG128 4.9 47.6 1.0

C.R.Butler, M.A.Brodney, E.M.Beck, G.Barreiro, C.E.Nolan, F.Pan, F.F.Vajdos, K.Parris, A.H.Varghese, C.J.Helal, R.Lira, S.D.Doran, D.Riddell, L.M.Buzon, J.K.Dutra, L.A.Martinez-Alsina, K.Ogilvie, J.C.Murray, J.M.Young, K.Atchison, A.Robshaw, C.Gonzales, J.Wang, Y.Zhang, B.T.O'neill. Discovery of A Series of Efficient, Centrally Efficacious BACE1 Inhibitors Through Structure-Based Drug Design. J.Med.Chem. 2015.
ISSN: ISSN 0022-2623
PubMed: 25695670
DOI: 10.1021/JM501833T