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Fluorine in PDB 4xrz: Human Cytochrome P450 2D6 BACE1 Inhibitor 6 Complex

Enzymatic activity of Human Cytochrome P450 2D6 BACE1 Inhibitor 6 Complex

All present enzymatic activity of Human Cytochrome P450 2D6 BACE1 Inhibitor 6 Complex:
1.14.14.1;

Protein crystallography data

The structure of Human Cytochrome P450 2D6 BACE1 Inhibitor 6 Complex, PDB code: 4xrz 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) 38.93 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.543, 192.480, 244.883, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 25.4

Other elements in 4xrz:

The structure of Human Cytochrome P450 2D6 BACE1 Inhibitor 6 Complex also contains other interesting chemical elements:

Zinc (Zn) 12 atoms
Iron (Fe) 4 atoms
Sodium (Na) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Cytochrome P450 2D6 BACE1 Inhibitor 6 Complex (pdb code 4xrz). 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 6 Complex, PDB code: 4xrz:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 4xrz

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Fluorine binding site 1 out of 8 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 6 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 6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:43.7
occ:1.00
 F1 A:SI6602 0.0 43.7 1.0
C6 A:SI6602 1.3 31.8 1.0
C5 A:SI6602 2.3 35.1 1.0
C1 A:SI6602 2.3 41.2 1.0
C A:GLY212 3.1 40.7 1.0
CA A:GLY212 3.2 40.1 1.0
O A:GLY212 3.4 37.4 1.0
N A:LEU213 3.4 45.9 1.0
O A:ALA209 3.5 35.2 1.0
C2 A:SI6602 3.6 33.1 1.0
C4 A:SI6602 3.6 42.8 1.0
CG A:GLN244 3.7 41.9 1.0
C3 A:SI6602 4.1 38.5 1.0
N A:GLY212 4.1 43.1 1.0
NE2 A:GLN244 4.2 40.7 1.0
O1 A:GOL606 4.2 44.8 1.0
CD A:GLN244 4.2 44.0 1.0
CA A:LEU213 4.2 42.0 1.0
C A:ALA209 4.3 36.0 1.0
CA A:ALA209 4.4 35.1 1.0
F2 A:SI6602 4.7 39.3 1.0
CB A:GLN244 4.7 42.2 1.0
O A:LEU208 4.8 40.7 1.0
C1 A:GOL606 4.8 47.9 1.0
CA A:GLN244 4.9 43.2 1.0
CB A:LEU213 4.9 37.9 1.0

Fluorine binding site 2 out of 8 in 4xrz

Go back to Fluorine Binding Sites List in 4xrz
Fluorine binding site 2 out of 8 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 6 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 6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:39.3
occ:1.00
 F2 A:SI6602 0.0 39.3 1.0
C4 A:SI6602 1.3 42.8 1.0
C5 A:SI6602 2.3 35.1 1.0
C3 A:SI6602 2.4 38.5 1.0
C7 A:SI6602 3.0 36.9 1.0
C11 A:SI6602 3.1 34.3 1.0
C8 A:SI6602 3.1 32.7 1.0
CG2 A:VAL308 3.3 38.9 1.0
CB A:SER304 3.4 28.0 1.0
O A:SER304 3.4 40.2 1.0
OG A:SER304 3.6 33.0 1.0
C6 A:SI6602 3.6 31.8 1.0
C2 A:SI6602 3.6 33.1 1.0
C A:SER304 3.6 35.5 1.0
CG1 A:VAL308 3.9 30.4 1.0
C12 A:SI6602 4.0 33.3 1.0
CA A:SER304 4.1 31.1 1.0
C1 A:SI6602 4.1 41.2 1.0
O1 A:SI6602 4.2 38.3 1.0
C9 A:SI6602 4.2 40.2 1.0
CB A:VAL308 4.2 33.0 1.0
N A:ALA305 4.2 29.2 1.0
C10 A:SI6602 4.2 36.7 1.0
CD1 A:LEU213 4.2 36.2 1.0
N1 A:SI6602 4.4 39.1 1.0
F1 A:SI6602 4.7 43.7 1.0
CA A:ALA305 4.7 38.4 1.0
O A:ALA209 4.8 35.2 1.0
CB A:LEU213 4.9 37.9 1.0

Fluorine binding site 3 out of 8 in 4xrz

Go back to Fluorine Binding Sites List in 4xrz
Fluorine binding site 3 out of 8 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 6 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 6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:51.4
occ:1.00
 F1 B:SI6602 0.0 51.4 1.0
C6 B:SI6602 1.3 39.7 1.0
C1 B:SI6602 2.3 37.5 1.0
C5 B:SI6602 2.3 39.5 1.0
C B:GLY212 3.0 43.9 1.0
CA B:GLY212 3.1 37.5 1.0
N B:LEU213 3.3 45.2 1.0
O B:GLY212 3.4 40.0 1.0
O B:ALA209 3.5 36.8 1.0
C2 B:SI6602 3.6 38.4 1.0
C4 B:SI6602 3.6 37.2 1.0
CG B:GLN244 3.8 47.2 1.0
CA B:LEU213 4.1 40.1 1.0
N B:GLY212 4.1 41.3 1.0
C3 B:SI6602 4.1 41.3 1.0
NE2 B:GLN244 4.3 41.2 1.0
CD B:GLN244 4.4 56.2 1.0
C B:ALA209 4.4 41.0 1.0
CA B:ALA209 4.5 38.6 1.0
F2 B:SI6602 4.7 35.6 1.0
O B:LEU208 4.7 44.3 1.0
O B:HOH778 4.7 37.0 1.0
CB B:LEU213 4.8 39.1 1.0
CB B:GLN244 4.8 47.0 1.0
CA B:GLN244 4.9 51.5 1.0

Fluorine binding site 4 out of 8 in 4xrz

Go back to Fluorine Binding Sites List in 4xrz
Fluorine binding site 4 out of 8 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 6 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 6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:35.6
occ:1.00
 F2 B:SI6602 0.0 35.6 1.0
C4 B:SI6602 1.3 37.2 1.0
C5 B:SI6602 2.3 39.5 1.0
C3 B:SI6602 2.4 41.3 1.0
C7 B:SI6602 3.0 31.5 1.0
C8 B:SI6602 3.1 33.1 1.0
C11 B:SI6602 3.1 29.9 1.0
CG2 B:VAL308 3.3 33.0 1.0
CB B:SER304 3.4 26.8 1.0
O B:SER304 3.5 41.7 1.0
C6 B:SI6602 3.6 39.7 1.0
C2 B:SI6602 3.6 38.4 1.0
OG B:SER304 3.7 36.5 1.0
C B:SER304 3.7 30.6 1.0
CG1 B:VAL308 3.8 28.2 1.0
C12 B:SI6602 4.0 37.5 1.0
C1 B:SI6602 4.1 37.5 1.0
CA B:SER304 4.1 32.3 1.0
O1 B:SI6602 4.2 36.6 1.0
CB B:VAL308 4.2 32.2 1.0
C9 B:SI6602 4.2 33.8 1.0
C10 B:SI6602 4.2 36.3 1.0
CD1 B:LEU213 4.3 32.7 1.0
N B:ALA305 4.3 33.9 1.0
N1 B:SI6602 4.4 37.8 1.0
F1 B:SI6602 4.7 51.4 1.0
CB B:LEU213 4.7 39.1 1.0
CA B:ALA305 4.8 37.0 1.0
O B:ALA209 4.9 36.8 1.0
CG B:LEU213 4.9 41.7 1.0

Fluorine binding site 5 out of 8 in 4xrz

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Fluorine binding site 5 out of 8 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 6 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 6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F602

b:56.8
occ:1.00
 F1 C:SI6602 0.0 56.8 1.0
C6 C:SI6602 1.3 44.1 1.0
C5 C:SI6602 2.3 30.1 1.0
C1 C:SI6602 2.3 49.3 1.0
C C:GLY212 3.0 47.2 1.0
N C:LEU213 3.2 52.2 1.0
CA C:GLY212 3.2 48.5 1.0
O C:GLY212 3.4 40.3 1.0
O C:ALA209 3.5 43.9 1.0
O C:HOH772 3.6 55.0 1.0
C4 C:SI6602 3.6 37.7 1.0
C2 C:SI6602 3.6 39.8 1.0
CG C:GLN244 3.7 46.4 1.0
CA C:LEU213 3.9 44.1 1.0
C3 C:SI6602 4.1 38.0 1.0
N C:GLY212 4.2 46.7 1.0
NE2 C:GLN244 4.3 43.1 1.0
CD C:GLN244 4.3 51.7 1.0
C C:ALA209 4.3 43.9 1.0
CA C:ALA209 4.5 37.2 1.0
F2 C:SI6602 4.6 35.9 1.0
O C:LEU208 4.7 46.6 1.0
CB C:LEU213 4.7 43.6 1.0
CB C:GLN244 4.8 46.3 1.0

Fluorine binding site 6 out of 8 in 4xrz

Go back to Fluorine Binding Sites List in 4xrz
Fluorine binding site 6 out of 8 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 6 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 6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F602

b:35.9
occ:1.00
 F2 C:SI6602 0.0 35.9 1.0
C4 C:SI6602 1.3 37.7 1.0
C5 C:SI6602 2.3 30.1 1.0
C3 C:SI6602 2.4 38.0 1.0
C7 C:SI6602 3.0 35.6 1.0
C11 C:SI6602 3.1 32.5 1.0
C8 C:SI6602 3.1 34.4 1.0
O C:SER304 3.3 44.7 1.0
CB C:SER304 3.3 27.0 1.0
CG1 C:VAL308 3.3 41.2 1.0
OG C:SER304 3.6 36.4 1.0
C6 C:SI6602 3.6 44.1 1.0
C C:SER304 3.6 34.8 1.0
C2 C:SI6602 3.6 39.8 1.0
C12 C:SI6602 3.9 37.2 1.0
CA C:SER304 4.0 35.6 1.0
CD2 C:LEU213 4.0 51.2 1.0
CB C:VAL308 4.1 37.0 1.0
C1 C:SI6602 4.1 49.3 1.0
O1 C:SI6602 4.2 38.0 1.0
C9 C:SI6602 4.2 35.0 1.0
C10 C:SI6602 4.2 36.4 1.0
N C:ALA305 4.2 33.3 1.0
N1 C:SI6602 4.4 42.6 1.0
CG C:LEU213 4.6 48.7 1.0
F1 C:SI6602 4.6 56.8 1.0
CA C:ALA305 4.7 35.2 1.0
CG2 C:VAL308 4.8 54.8 1.0
CB C:LEU213 4.8 43.6 1.0
O C:ALA209 5.0 43.9 1.0

Fluorine binding site 7 out of 8 in 4xrz

Go back to Fluorine Binding Sites List in 4xrz
Fluorine binding site 7 out of 8 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 6 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 6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F602

b:45.0
occ:1.00
 F1 D:SI6602 0.0 45.0 1.0
C6 D:SI6602 1.3 34.0 1.0
C1 D:SI6602 2.3 36.7 1.0
C5 D:SI6602 2.3 40.3 1.0
C D:GLY212 3.0 41.4 1.0
N D:LEU213 3.2 40.1 1.0
CA D:GLY212 3.3 42.1 1.0
O D:GLY212 3.3 39.1 1.0
O D:ALA209 3.5 38.8 1.0
C2 D:SI6602 3.6 37.5 1.0
C4 D:SI6602 3.6 36.4 1.0
C3 D:GOL606 3.7 51.6 1.0
CG D:GLN244 3.8 40.8 1.0
CA D:LEU213 3.9 42.5 1.0
C3 D:SI6602 4.1 31.4 1.0
O3 D:GOL606 4.1 53.1 1.0
N D:GLY212 4.2 43.8 1.0
C D:ALA209 4.4 38.8 1.0
CD D:GLN244 4.4 49.4 1.0
NE2 D:GLN244 4.4 33.8 1.0
CA D:ALA209 4.5 37.4 1.0
F2 D:SI6602 4.7 38.6 1.0
CB D:LEU213 4.7 41.0 1.0
O D:LEU208 4.7 44.7 1.0
C2 D:GOL606 4.9 48.1 1.0
CB D:GLN244 4.9 41.2 1.0

Fluorine binding site 8 out of 8 in 4xrz

Go back to Fluorine Binding Sites List in 4xrz
Fluorine binding site 8 out of 8 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 6 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 6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F602

b:38.6
occ:1.00
 F2 D:SI6602 0.0 38.6 1.0
C4 D:SI6602 1.3 36.4 1.0
C5 D:SI6602 2.3 40.3 1.0
C3 D:SI6602 2.4 31.4 1.0
C7 D:SI6602 3.0 35.8 1.0
C11 D:SI6602 3.1 32.1 1.0
C8 D:SI6602 3.1 32.9 1.0
O D:SER304 3.3 37.1 1.0
CB D:SER304 3.4 26.6 1.0
CG1 D:VAL308 3.4 44.8 1.0
OG D:SER304 3.5 31.4 1.0
C6 D:SI6602 3.6 34.0 1.0
C D:SER304 3.6 34.4 1.0
C2 D:SI6602 3.6 37.5 1.0
C12 D:SI6602 4.0 30.1 1.0
CA D:SER304 4.0 33.7 1.0
CD1 D:LEU213 4.1 39.9 1.0
C1 D:SI6602 4.1 36.7 1.0
O1 D:SI6602 4.2 36.3 1.0
C9 D:SI6602 4.2 30.2 1.0
N D:ALA305 4.2 31.2 1.0
CB D:VAL308 4.2 33.5 1.0
C10 D:SI6602 4.2 36.2 1.0
N1 D:SI6602 4.4 41.1 1.0
F1 D:SI6602 4.7 45.0 1.0
CA D:ALA305 4.7 37.4 1.0
CB D:LEU213 4.8 41.0 1.0
O D:ALA209 5.0 38.8 1.0
CG D:LEU213 5.0 43.7 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: Thu Aug 1 06:44:40 2024

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