Fluorine in PDB 5tfu: Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex

All present enzymatic activity of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex:
1.14.14.1;

The structure of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex, PDB code: 5tfu was solved by M.H.Hsu, E.F.Johnson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.07 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.105, 191.756, 246.838, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 25

The structure of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex also contains other interesting chemical elements:

Iron	(Fe)	4 atoms
Zinc	(Zn)	5 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Fluorine atom in the Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex (pdb code 5tfu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 20 binding sites of Fluorine where determined in the Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex, PDB code: 5tfu:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 20 in the Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F604 b:75.3 occ:1.00 F1 A:P6M604 0.0 75.3 1.0 C7 A:P6M604 1.4 69.6 1.0 C8 A:P6M604 2.3 63.0 1.0 C6 A:P6M604 2.4 72.0 1.0 C10 A:P6M604 2.9 67.3 1.0 C15 A:P6M604 3.0 65.1 1.0 C11 A:P6M604 3.1 48.0 1.0 C9 A:P6M604 3.6 67.2 1.0 CD1 A:LEU213 3.6 56.7 1.0 C5 A:P6M604 3.6 62.8 1.0 C12 A:P6M604 3.9 56.9 1.0 CB A:LEU213 4.0 63.0 1.0 C4 A:P6M604 4.1 64.4 1.0 CA A:LEU213 4.2 67.1 1.0 CB A:SER304 4.3 41.4 1.0 N1 A:P6M604 4.3 69.4 1.0 CG A:LEU213 4.3 55.0 1.0 CG1 A:VAL308 4.4 37.5 1.0 N A:LEU213 4.6 70.7 1.0 F A:P6M604 4.7 56.4 1.0 O A:SER304 4.7 64.9 1.0 O A:ALA209 4.7 57.6 1.0 OG A:SER304 4.8 48.3 1.0 C14 A:P6M604 4.8 51.3 1.0 CD2 A:LEU213 4.9 48.9 1.0 C A:SER304 5.0 54.9 1.0

Fluorine binding site 2 out of 20 in the Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F604 b:56.4 occ:1.00 F A:P6M604 0.0 56.4 1.0 C9 A:P6M604 1.4 67.2 1.0 C4 A:P6M604 2.3 64.4 1.0 C8 A:P6M604 2.3 63.0 1.0 C3 A:P6M604 2.8 65.1 1.0 C7 A:P6M604 3.6 69.6 1.0 C5 A:P6M604 3.6 62.8 1.0 CA A:ALA209 3.7 53.9 1.0 CD2 A:PHE247 3.7 41.3 1.0 O A:ALA209 3.7 57.6 1.0 CG A:PHE247 3.9 42.8 1.0 N A:P6M604 4.0 53.5 1.0 CE2 A:PHE247 4.0 41.3 1.0 C6 A:P6M604 4.1 72.0 1.0 C A:ALA209 4.2 56.4 1.0 CA A:GLY212 4.2 59.6 1.0 CB A:ALA209 4.3 59.2 1.0 CB A:SER304 4.4 41.4 1.0 CD1 A:PHE247 4.4 52.4 1.0 CB A:PHE247 4.4 50.6 1.0 CZ A:PHE247 4.5 47.8 1.0 O A:LEU208 4.5 64.5 1.0 C A:GLY212 4.6 65.8 1.0 CE1 A:PHE247 4.7 49.9 1.0 F1 A:P6M604 4.7 75.3 1.0 CG A:GLN244 4.7 64.5 1.0 C A:P6M604 4.7 66.5 1.0 N A:ALA209 4.7 56.4 1.0 N A:GLY212 4.9 58.1 1.0 N A:LEU213 4.9 70.7 1.0 C1 A:P6M604 4.9 69.3 1.0 C2 A:P6M604 4.9 71.8 1.0 O A:GLY212 5.0 71.1 1.0

Fluorine binding site 3 out of 20 in the Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F604 b:79.8 occ:1.00 F2 A:P6M604 0.0 79.8 1.0 C16 A:P6M604 1.3 79.2 1.0 F4 A:P6M604 2.1 88.4 1.0 F3 A:P6M604 2.1 61.4 1.0 C1 A:P6M604 2.4 69.3 1.0 N A:P6M604 2.9 53.5 1.0 C A:P6M604 3.2 66.5 1.0 OD2 A:ASP301 3.5 38.0 1.0 CB A:ALA300 3.6 36.8 1.0 C2 A:P6M604 3.7 71.8 1.0 O A:ILE297 4.0 42.8 1.0 CG2 A:ILE297 4.2 40.0 1.0 C3 A:P6M604 4.4 65.1 1.0 CZ A:PHE112 4.5 52.5 1.0 N A:ASP301 4.5 41.2 1.0 C A:ALA300 4.5 37.8 1.0 CE2 A:PHE112 4.5 57.4 1.0 CG A:ASP301 4.5 41.0 1.0 CA A:ILE297 4.6 41.0 1.0 CA A:ALA300 4.7 28.8 1.0 C A:ILE297 4.8 43.1 1.0 O A:ALA300 4.9 45.6 1.0 CB A:ILE297 4.9 32.8 1.0

Fluorine binding site 4 out of 20 in the Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F604 b:61.4 occ:1.00 F3 A:P6M604 0.0 61.4 1.0 C16 A:P6M604 1.3 79.2 1.0 F2 A:P6M604 2.1 79.8 1.0 F4 A:P6M604 2.1 88.4 1.0 C1 A:P6M604 2.4 69.3 1.0 C A:P6M604 2.8 66.5 1.0 C2 A:P6M604 2.9 71.8 1.0 CD1 A:LEU248 3.5 58.0 1.0 CG A:LEU248 3.6 51.4 1.0 N A:P6M604 3.7 53.5 1.0 CD2 A:LEU248 4.1 42.6 1.0 CE2 A:PHE112 4.1 57.4 1.0 CB A:LEU110 4.1 62.1 1.0 CD1 A:LEU110 4.1 63.1 1.0 CB A:ALA300 4.4 36.8 1.0 CG1 A:ILE297 4.5 29.2 1.0 CG A:LEU110 4.6 62.8 1.0 CG2 A:ILE297 4.7 40.0 1.0 CZ A:PHE112 4.7 52.5 1.0 O A:LEU110 4.7 60.8 1.0 CA A:ILE297 4.7 41.0 1.0 C3 A:P6M604 4.8 65.1 1.0 CB A:ILE297 4.9 32.8 1.0 CD2 A:LEU110 5.0 65.3 1.0 CB A:LEU248 5.0 49.6 1.0

Fluorine binding site 5 out of 20 in the Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F604 b:88.4 occ:1.00 F4 A:P6M604 0.0 88.4 1.0 C16 A:P6M604 1.3 79.2 1.0 F2 A:P6M604 2.1 79.8 1.0 F3 A:P6M604 2.1 61.4 1.0 C1 A:P6M604 2.4 69.3 1.0 N A:P6M604 2.9 53.5 1.0 CD1 A:LEU110 3.2 63.1 1.0 C2 A:P6M604 3.2 71.8 1.0 CE2 A:PHE112 3.5 57.4 1.0 C A:P6M604 3.7 66.5 1.0 CZ A:PHE112 3.8 52.5 1.0 C3 A:P6M604 4.2 65.1 1.0 CG A:LEU110 4.3 62.8 1.0 CB A:LEU110 4.3 62.1 1.0 OE1 A:GLN244 4.5 64.0 1.0 CD2 A:PHE112 4.7 61.4 1.0 N2 A:P6M604 4.9 46.5 1.0 OD2 A:ASP301 4.9 38.0 1.0 CD2 A:LEU110 5.0 65.3 1.0

Fluorine binding site 6 out of 20 in the Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F603 b:78.0 occ:1.00 F1 B:P6M603 0.0 78.0 1.0 C7 B:P6M603 1.4 70.1 1.0 C8 B:P6M603 2.3 59.5 1.0 C6 B:P6M603 2.4 62.7 1.0 C10 B:P6M603 2.9 52.2 1.0 C15 B:P6M603 2.9 54.6 1.0 C11 B:P6M603 3.2 43.6 1.0 C9 B:P6M603 3.6 58.6 1.0 C5 B:P6M603 3.6 61.1 1.0 CD1 B:LEU213 3.8 52.5 1.0 CB B:SER304 4.0 41.0 1.0 C12 B:P6M603 4.1 40.0 1.0 CG1 B:VAL308 4.1 48.6 1.0 C4 B:P6M603 4.1 61.4 1.0 CB B:LEU213 4.1 53.2 1.0 N1 B:P6M603 4.3 65.3 1.0 CG B:LEU213 4.5 53.5 1.0 CA B:LEU213 4.5 65.9 1.0 OG B:SER304 4.5 38.3 1.0 O B:SER304 4.6 60.4 1.0 C B:SER304 4.7 53.2 1.0 F B:P6M603 4.7 55.7 1.0 CD2 B:LEU213 4.9 53.1 1.0 CA B:SER304 4.9 43.7 1.0 N B:LEU213 4.9 64.4 1.0 C14 B:P6M603 5.0 44.9 1.0

Fluorine binding site 7 out of 20 in the Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F603 b:55.7 occ:1.00 F B:P6M603 0.0 55.7 1.0 C9 B:P6M603 1.4 58.6 1.0 C4 B:P6M603 2.3 61.4 1.0 C8 B:P6M603 2.3 59.5 1.0 C3 B:P6M603 2.8 70.3 1.0 N B:P6M603 3.4 70.3 1.0 O B:ALA209 3.5 51.6 1.0 C7 B:P6M603 3.6 70.1 1.0 C5 B:P6M603 3.6 61.1 1.0 CA B:ALA209 3.6 46.0 1.0 CD2 B:PHE247 4.0 44.3 1.0 CA B:GLY212 4.0 61.5 1.0 C B:ALA209 4.0 50.8 1.0 CG B:PHE247 4.1 37.1 1.0 C6 B:P6M603 4.1 62.7 1.0 CB B:ALA209 4.2 47.9 1.0 CE2 B:PHE247 4.3 43.6 1.0 CB B:SER304 4.3 41.0 1.0 O B:LEU208 4.3 44.7 1.0 C B:GLY212 4.4 61.1 1.0 CD1 B:PHE247 4.5 42.3 1.0 N B:LEU213 4.6 64.4 1.0 CB B:PHE247 4.6 47.0 1.0 CZ B:PHE247 4.6 36.0 1.0 N B:ALA209 4.7 50.0 1.0 F1 B:P6M603 4.7 78.0 1.0 N B:GLY212 4.7 48.6 1.0 CE1 B:PHE247 4.7 36.4 1.0 C1 B:P6M603 4.8 68.1 1.0 CG B:GLN244 4.9 63.5 1.0 C B:LEU208 4.9 52.3 1.0 O B:GLY212 4.9 67.6 1.0

Fluorine binding site 8 out of 20 in the Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F603 b:59.8 occ:1.00 F2 B:P6M603 0.0 59.8 1.0 C16 B:P6M603 1.3 69.2 1.0 F3 B:P6M603 2.1 74.7 1.0 F4 B:P6M603 2.1 73.8 1.0 C1 B:P6M603 2.4 68.1 1.0 N B:P6M603 2.9 70.3 1.0 C B:P6M603 3.3 54.2 1.0 OD2 B:ASP301 3.4 26.9 1.0 C2 B:P6M603 3.7 68.2 1.0 CB B:ALA300 3.8 34.6 1.0 C3 B:P6M603 3.9 70.3 1.0 S B:P6M603 4.1 52.5 1.0 N B:ASP301 4.4 38.3 1.0 C B:ALA300 4.4 34.8 1.0 CG B:ASP301 4.5 31.8 1.0 C4 B:P6M603 4.6 61.4 1.0 C5 B:P6M603 4.6 61.1 1.0 O B:ILE297 4.6 31.3 1.0 CA B:ASP301 4.8 28.6 1.0 CA B:ALA300 4.8 29.2 1.0 O B:ALA300 4.8 40.2 1.0 C13 B:P6M603 4.8 54.5 1.0 N2 B:P6M603 4.9 55.3 1.0 CG2 B:ILE297 4.9 30.3 1.0

Fluorine binding site 9 out of 20 in the Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F603 b:74.7 occ:1.00 F3 B:P6M603 0.0 74.7 1.0 C16 B:P6M603 1.3 69.2 1.0 F2 B:P6M603 2.1 59.8 1.0 F4 B:P6M603 2.1 73.8 1.0 C1 B:P6M603 2.4 68.1 1.0 C B:P6M603 2.8 54.2 1.0 C2 B:P6M603 2.9 68.2 1.0 CD1 B:LEU110 3.5 55.9 1.0 N B:P6M603 3.7 70.3 1.0 CE2 B:PHE112 4.2 54.4 1.0 CB B:LEU110 4.2 54.3 1.0 CG B:LEU110 4.4 66.5 1.0 CD2 B:LEU248 4.5 32.1 1.0 CB B:ALA300 4.5 34.6 1.0 C3 B:P6M603 4.5 70.3 1.0 CZ B:PHE112 4.7 47.4 1.0 CD1 B:LEU248 4.8 37.5 1.0 CG2 B:ILE297 4.8 30.3 1.0 CD2 B:LEU110 4.9 67.3 1.0

Fluorine binding site 10 out of 20 in the Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F603 b:73.8 occ:1.00 F4 B:P6M603 0.0 73.8 1.0 C16 B:P6M603 1.3 69.2 1.0 F3 B:P6M603 2.1 74.7 1.0 F2 B:P6M603 2.1 59.8 1.0 C1 B:P6M603 2.4 68.1 1.0 N B:P6M603 3.0 70.3 1.0 C2 B:P6M603 3.2 68.2 1.0 C3 B:P6M603 3.3 70.3 1.0 CD1 B:LEU110 3.3 55.9 1.0 OE1 B:GLN244 3.5 57.9 1.0 C B:P6M603 3.7 54.2 1.0 N2 B:P6M603 4.1 55.3 1.0 C5 B:P6M603 4.1 61.1 1.0 C4 B:P6M603 4.2 61.4 1.0 C13 B:P6M603 4.4 54.5 1.0 CD B:GLN244 4.4 66.8 1.0 S B:P6M603 4.6 52.5 1.0 CG B:LEU110 4.6 66.5 1.0 OD2 B:ASP301 5.0 26.9 1.0

C.R.Butler, K.Ogilvie, L.Martinez-Alsina, G.Barreiro, E.M.Beck, C.E.Nolan, K.Atchison, E.Benvenuti, L.Buzon, S.Doran, C.Gonzales, C.J.Helal, X.Hou, M.H.Hsu, E.F.Johnson, K.Lapham, L.Lanyon, K.Parris, B.T.O'neill, D.Riddell, A.Robshaw, F.Vajdos, M.A.Brodney. Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality. J. Med. Chem. V. 60 386 2017.
ISSN: ISSN 1520-4804
PubMed: 27997172
DOI: 10.1021/ACS.JMEDCHEM.6B01451