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Fluorine in PDB 4xry: Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex

Enzymatic activity of Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex

All present enzymatic activity of Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex:
1.14.14.1;

Protein crystallography data

The structure of Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex, PDB code: 4xry was solved by E.F.Johnson, Y.Fan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.16 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.064, 192.341, 247.304, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.1

Other elements in 4xry:

The structure of Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Zinc (Zn) 17 atoms

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 8 in 4xry

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Fluorine binding site 1 out of 8 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:89.7
occ:1.00
 F1 A:SI5602 0.0 89.7 1.0
C6 A:SI5602 1.4 86.1 1.0
C5 A:SI5602 2.3 81.4 1.0
C1 A:SI5602 2.4 87.2 1.0
C11 A:SI5602 2.9 88.4 1.0
C7 A:SI5602 2.9 89.2 1.0
C12 A:SI5602 3.2 81.7 1.0
CB A:SER304 3.4 48.0 1.0
C4 A:SI5602 3.6 79.4 1.0
C2 A:SI5602 3.6 77.8 1.0
CD1 A:LEU213 3.9 76.3 1.0
OG A:SER304 4.0 59.8 1.0
O1 A:SI5602 4.0 83.1 1.0
C8 A:SI5602 4.0 76.3 1.0
C3 A:SI5602 4.1 81.1 1.0
O A:ALA209 4.1 66.0 1.0
CB A:LEU213 4.2 69.0 1.0
C13 A:SI5602 4.3 72.6 1.0
C9 A:SI5602 4.3 73.4 1.0
N1 A:SI5602 4.3 83.9 1.0
CA A:SER304 4.4 44.9 1.0
O A:SER304 4.4 71.5 1.0
C A:SER304 4.4 63.6 1.0
CG A:LEU213 4.5 73.5 1.0
CA A:LEU213 4.6 76.3 1.0
CG1 A:VAL308 4.6 45.0 1.0
F2 A:SI5602 4.7 69.3 1.0
N A:LEU213 4.8 76.7 1.0

Fluorine binding site 2 out of 8 in 4xry

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Fluorine binding site 2 out of 8 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:69.3
occ:1.00
 F2 A:SI5602 0.0 69.3 1.0
C4 A:SI5602 1.4 79.4 1.0
C3 A:SI5602 2.3 81.1 1.0
C5 A:SI5602 2.3 81.4 1.0
OE1 A:GLN244 3.5 85.7 1.0
C6 A:SI5602 3.6 86.1 1.0
C2 A:SI5602 3.6 77.8 1.0
CA A:GLY212 3.8 66.0 1.0
CD2 A:PHE247 3.8 36.5 1.0
CD A:GLN244 3.9 72.8 1.0
CG A:PHE247 4.0 40.4 1.0
O A:ALA209 4.1 66.0 1.0
C1 A:SI5602 4.1 87.2 1.0
CB A:PHE247 4.1 44.2 1.0
C A:GLY212 4.2 80.6 1.0
CA A:GLN244 4.3 61.3 1.0
CA A:ALA209 4.3 57.4 1.0
O A:LEU208 4.4 58.4 1.0
NE2 A:GLN244 4.4 63.5 1.0
CE2 A:PHE247 4.4 41.9 1.0
N A:LEU213 4.6 76.7 1.0
N A:GLY212 4.6 71.8 1.0
C A:ALA209 4.6 67.1 1.0
CG A:GLN244 4.6 65.8 1.0
F1 A:SI5602 4.7 89.7 1.0
CB A:GLN244 4.7 65.3 1.0
O A:PHE243 4.7 60.5 1.0
O A:GLY212 4.8 82.7 1.0
CD1 A:PHE247 4.8 49.1 1.0
N A:GLN244 4.9 62.4 1.0

Fluorine binding site 3 out of 8 in 4xry

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Fluorine binding site 3 out of 8 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:86.8
occ:1.00
 F1 B:SI5602 0.0 86.8 1.0
C6 B:SI5602 1.4 78.4 1.0
C5 B:SI5602 2.3 67.1 1.0
C1 B:SI5602 2.4 76.5 1.0
C11 B:SI5602 2.9 77.0 1.0
C7 B:SI5602 3.0 80.1 1.0
CB B:SER304 3.1 52.2 1.0
C12 B:SI5602 3.2 77.1 1.0
C4 B:SI5602 3.6 78.5 1.0
C2 B:SI5602 3.6 66.1 1.0
OG B:SER304 3.9 60.5 1.0
C8 B:SI5602 4.0 74.2 1.0
O1 B:SI5602 4.0 76.1 1.0
CB B:LEU213 4.1 63.3 1.0
O B:SER304 4.1 80.0 1.0
C3 B:SI5602 4.1 74.6 1.0
C B:SER304 4.1 70.8 1.0
CA B:SER304 4.1 46.5 1.0
O B:ALA209 4.1 63.3 1.0
C13 B:SI5602 4.2 67.1 1.0
C9 B:SI5602 4.2 71.6 1.0
N1 B:SI5602 4.3 71.7 1.0
CG1 B:VAL308 4.5 57.6 1.0
CA B:LEU213 4.5 70.0 1.0
CD1 B:LEU213 4.6 78.2 1.0
F2 B:SI5602 4.7 70.8 1.0
N B:LEU213 4.7 73.1 1.0
N B:ALA305 4.7 64.5 1.0
CG B:LEU213 4.8 73.7 1.0

Fluorine binding site 4 out of 8 in 4xry

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Fluorine binding site 4 out of 8 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:70.8
occ:1.00
 F2 B:SI5602 0.0 70.8 1.0
C4 B:SI5602 1.4 78.5 1.0
C3 B:SI5602 2.3 74.6 1.0
C5 B:SI5602 2.3 67.1 1.0
CA B:GLY212 3.5 69.9 1.0
C6 B:SI5602 3.6 78.4 1.0
C2 B:SI5602 3.6 66.1 1.0
CD2 B:PHE247 3.7 38.8 1.0
CG B:GLN244 3.8 65.3 1.0
C B:GLY212 3.8 74.9 1.0
CG B:PHE247 4.0 38.7 1.0
O B:ALA209 4.1 63.3 1.0
C1 B:SI5602 4.1 76.5 1.0
CA B:GLN244 4.1 59.6 1.0
CB B:PHE247 4.2 43.7 1.0
CA B:ALA209 4.2 49.1 1.0
CB B:GLN244 4.3 64.9 1.0
O B:GLY212 4.3 74.5 1.0
CE2 B:PHE247 4.3 43.6 1.0
N B:LEU213 4.3 73.1 1.0
CD B:GLN244 4.3 69.5 1.0
O B:LEU208 4.4 59.6 1.0
N B:GLY212 4.4 66.1 1.0
C B:ALA209 4.6 61.7 1.0
F1 B:SI5602 4.7 86.8 1.0
NE2 B:GLN244 4.7 69.9 1.0
CD1 B:PHE247 4.8 38.1 1.0
OE1 B:GLN244 4.9 74.8 1.0
O B:GLN244 4.9 52.7 1.0
N B:GLN244 5.0 54.6 1.0

Fluorine binding site 5 out of 8 in 4xry

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Fluorine binding site 5 out of 8 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F602

b:71.4
occ:1.00
 F1 C:SI5602 0.0 71.4 1.0
C6 C:SI5602 1.4 76.0 1.0
C5 C:SI5602 2.3 73.3 1.0
C1 C:SI5602 2.4 77.2 1.0
OG C:SER304 2.5 82.9 1.0
C7 C:SI5602 2.9 83.7 1.0
C11 C:SI5602 2.9 82.6 1.0
C12 C:SI5602 3.2 85.3 1.0
C4 C:SI5602 3.6 72.5 1.0
C2 C:SI5602 3.6 72.9 1.0
CD1 C:LEU213 3.8 82.2 1.0
CB C:SER304 3.8 44.5 1.0
O C:ALA209 3.9 64.7 1.0
CB C:LEU213 4.0 63.1 1.0
O1 C:SI5602 4.0 75.5 1.0
C8 C:SI5602 4.0 70.3 1.0
C3 C:SI5602 4.1 75.7 1.0
C13 C:SI5602 4.2 77.3 1.0
C9 C:SI5602 4.3 74.2 1.0
N1 C:SI5602 4.3 77.9 1.0
CG C:LEU213 4.3 83.7 1.0
CA C:LEU213 4.4 69.2 1.0
CG1 C:VAL308 4.5 56.5 1.0
N C:LEU213 4.6 74.0 1.0
F2 C:SI5602 4.7 65.7 1.0
C C:SER304 4.8 60.5 1.0
CA C:SER304 4.8 47.9 1.0
O C:SER304 4.8 61.9 1.0
C C:ALA209 4.9 65.0 1.0

Fluorine binding site 6 out of 8 in 4xry

Go back to Fluorine Binding Sites List in 4xry
Fluorine binding site 6 out of 8 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F602

b:65.7
occ:1.00
 F2 C:SI5602 0.0 65.7 1.0
C4 C:SI5602 1.4 72.5 1.0
C5 C:SI5602 2.3 73.3 1.0
C3 C:SI5602 2.3 75.7 1.0
CA C:GLY212 3.5 67.9 1.0
CG C:GLN244 3.5 63.6 1.0
C6 C:SI5602 3.6 76.0 1.0
C2 C:SI5602 3.6 72.9 1.0
C C:GLY212 3.9 68.2 1.0
CA C:GLN244 4.0 59.2 1.0
CD2 C:PHE247 4.1 39.1 1.0
CB C:GLN244 4.1 66.3 1.0
C1 C:SI5602 4.1 77.2 1.0
CB C:PHE247 4.1 46.1 1.0
O C:ALA209 4.1 64.7 1.0
O C:LEU208 4.2 68.1 1.0
CG C:PHE247 4.2 45.3 1.0
O C:GLY212 4.3 73.0 1.0
CD C:GLN244 4.3 72.2 1.0
N C:LEU213 4.3 74.0 1.0
N C:GLY212 4.4 71.7 1.0
CA C:ALA209 4.4 52.2 1.0
NE2 C:GLN244 4.6 71.7 1.0
F1 C:SI5602 4.7 71.4 1.0
N C:GLN244 4.7 53.4 1.0
C C:ALA209 4.7 65.0 1.0
CE2 C:PHE247 4.8 48.8 1.0
O C:PHE243 4.8 60.7 1.0
CD1 C:PHE247 4.9 46.4 1.0

Fluorine binding site 7 out of 8 in 4xry

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Fluorine binding site 7 out of 8 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F602

b:85.2
occ:1.00
 F1 D:SI5602 0.0 85.2 1.0
C6 D:SI5602 1.4 81.4 1.0
C5 D:SI5602 2.3 75.7 1.0
C1 D:SI5602 2.4 85.6 1.0
C11 D:SI5602 2.9 84.2 1.0
C7 D:SI5602 3.0 84.0 1.0
CB D:SER304 3.1 47.1 1.0
C12 D:SI5602 3.2 80.6 1.0
OG D:SER304 3.5 52.6 1.0
C4 D:SI5602 3.6 73.4 1.0
C2 D:SI5602 3.6 74.8 1.0
CD1 D:LEU213 3.8 81.9 1.0
C8 D:SI5602 4.0 76.1 1.0
O1 D:SI5602 4.0 84.3 1.0
O D:SER304 4.1 76.9 1.0
C3 D:SI5602 4.1 75.1 1.0
C D:SER304 4.1 65.9 1.0
C13 D:SI5602 4.1 63.4 1.0
CA D:SER304 4.1 44.4 1.0
C9 D:SI5602 4.2 75.4 1.0
CB D:LEU213 4.2 65.9 1.0
O D:ALA209 4.3 66.2 1.0
N1 D:SI5602 4.3 78.6 1.0
CG1 D:VAL308 4.6 61.3 1.0
CG D:LEU213 4.6 76.2 1.0
CA D:LEU213 4.7 72.3 1.0
F2 D:SI5602 4.7 69.0 1.0
N D:ALA305 4.7 55.6 1.0
N D:LEU213 4.9 73.9 1.0

Fluorine binding site 8 out of 8 in 4xry

Go back to Fluorine Binding Sites List in 4xry
Fluorine binding site 8 out of 8 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F602

b:69.0
occ:1.00
 F2 D:SI5602 0.0 69.0 1.0
C4 D:SI5602 1.4 73.4 1.0
C3 D:SI5602 2.3 75.1 1.0
C5 D:SI5602 2.3 75.7 1.0
C6 D:SI5602 3.6 81.4 1.0
C2 D:SI5602 3.6 74.8 1.0
CA D:GLY212 3.7 68.0 1.0
CG D:GLN244 3.7 70.5 1.0
CD2 D:PHE247 3.7 40.4 1.0
C D:GLY212 3.9 73.1 1.0
CA D:GLN244 4.0 63.8 1.0
O D:ALA209 4.0 66.2 1.0
CG D:PHE247 4.0 41.3 1.0
C1 D:SI5602 4.1 85.6 1.0
CB D:GLN244 4.2 69.9 1.0
O D:GLY212 4.2 70.2 1.0
CB D:PHE247 4.2 50.0 1.0
CE2 D:PHE247 4.3 44.9 1.0
CA D:ALA209 4.4 57.9 1.0
N D:LEU213 4.4 73.9 1.0
CD D:GLN244 4.5 66.3 1.0
O D:LEU208 4.5 57.0 1.0
N D:GLY212 4.6 63.7 1.0
C D:ALA209 4.7 68.6 1.0
F1 D:SI5602 4.7 85.2 1.0
CD1 D:PHE247 4.8 44.5 1.0
N D:GLN244 4.8 57.4 1.0
O D:GLN244 4.9 58.7 1.0
NE2 D:GLN244 4.9 65.6 1.0
C D:GLN244 5.0 65.1 1.0

Reference:

M.A.Brodney, E.M.Beck, C.R.Butler, G.Barreiro, E.F.Johnson, D.Riddell, K.Parris, C.E.Nolan, Y.Fan, K.Atchison, C.Gonzales, A.E.Robshaw, S.D.Doran, M.W.Bundesmann, L.Buzon, J.Dutra, K.Henegar, E.Lachapelle, X.Hou, B.N.Rogers, J.Pandit, R.Lira, L.Martinez-Alsina, P.Mikochik, J.C.Murray, K.Ogilvie, L.Price, S.M.Sakya, A.Yu, Y.Zhang, B.T.O'neill. Utilizing Structures of CYP2D6 and BACE1 Complexes to Reduce Risk of Drug-Drug Interactions with A Novel Series of Centrally Efficacious BACE1 Inhibitors. J.Med.Chem. V. 58 3223 2015.
ISSN: ISSN 0022-2623
PubMed: 25781223
DOI: 10.1021/ACS.JMEDCHEM.5B00191
Page generated: Sun Dec 13 12:15:12 2020

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