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Iron 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:

Fluorine (F) 8 atoms
Zinc (Zn) 12 atoms
Sodium (Na) 4 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron where determined in the Human Cytochrome P450 2D6 BACE1 Inhibitor 6 Complex, PDB code: 4xrz:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4xrz

Go back to Iron Binding Sites List in 4xrz
Iron binding site 1 out of 4 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 6 Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe601

b:22.7
occ:1.00
FE A:HEM601 0.0 22.7 1.0
NB A:HEM601 2.0 31.9 1.0
N4 A:SI6602 2.0 22.1 1.0
NA A:HEM601 2.0 25.5 1.0
ND A:HEM601 2.1 28.3 1.0
NC A:HEM601 2.1 26.8 1.0
SG A:CYS443 2.3 26.4 1.0
C4A A:HEM601 3.0 25.0 1.0
C1B A:HEM601 3.0 25.2 1.0
C16 A:SI6602 3.0 31.0 1.0
C4B A:HEM601 3.0 27.8 1.0
N3 A:SI6602 3.1 34.6 1.0
C1A A:HEM601 3.1 27.7 1.0
C1C A:HEM601 3.1 28.8 1.0
C4D A:HEM601 3.1 21.8 1.0
C1D A:HEM601 3.1 27.7 1.0
C4C A:HEM601 3.1 29.7 1.0
CB A:CYS443 3.2 23.8 1.0
CHB A:HEM601 3.4 24.5 1.0
CHC A:HEM601 3.4 28.4 1.0
CHA A:HEM601 3.4 29.6 1.0
CHD A:HEM601 3.5 25.1 1.0
CA A:CYS443 4.1 29.2 1.0
C3A A:HEM601 4.3 26.8 1.0
C2A A:HEM601 4.3 24.6 1.0
C15 A:SI6602 4.3 33.4 1.0
C2B A:HEM601 4.3 27.3 1.0
C3B A:HEM601 4.3 32.1 1.0
C14 A:SI6602 4.3 32.6 1.0
C3D A:HEM601 4.3 27.6 1.0
C2C A:HEM601 4.3 30.8 1.0
C2D A:HEM601 4.3 27.4 1.0
C3C A:HEM601 4.3 32.6 1.0
CZ A:PHE120 4.8 39.9 1.0
C A:CYS443 4.9 25.8 1.0
N A:GLY445 5.0 28.4 1.0
CE1 A:PHE120 5.0 37.9 1.0

Iron binding site 2 out of 4 in 4xrz

Go back to Iron Binding Sites List in 4xrz
Iron binding site 2 out of 4 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 6 Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Human Cytochrome P450 2D6 BACE1 Inhibitor 6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:22.5
occ:1.00
FE B:HEM601 0.0 22.5 1.0
NB B:HEM601 2.0 30.3 1.0
NA B:HEM601 2.0 23.9 1.0
ND B:HEM601 2.1 31.6 1.0
NC B:HEM601 2.1 24.3 1.0
N4 B:SI6602 2.1 18.4 1.0
SG B:CYS443 2.2 25.9 1.0
C4A B:HEM601 3.0 26.1 1.0
C1B B:HEM601 3.1 31.1 1.0
C4B B:HEM601 3.1 29.6 1.0
C1A B:HEM601 3.1 32.6 1.0
C1C B:HEM601 3.1 28.0 1.0
C4D B:HEM601 3.1 25.6 1.0
N3 B:SI6602 3.1 31.1 1.0
C1D B:HEM601 3.1 29.6 1.0
C4C B:HEM601 3.1 29.5 1.0
C16 B:SI6602 3.1 24.7 1.0
CB B:CYS443 3.3 28.2 1.0
CHB B:HEM601 3.4 27.5 1.0
CHC B:HEM601 3.4 28.1 1.0
CHA B:HEM601 3.4 35.4 1.0
CHD B:HEM601 3.5 29.7 1.0
CA B:CYS443 4.1 28.6 1.0
C3A B:HEM601 4.3 28.0 1.0
C2A B:HEM601 4.3 37.1 1.0
C2B B:HEM601 4.3 33.8 1.0
C3B B:HEM601 4.3 33.9 1.0
C15 B:SI6602 4.3 25.6 1.0
C3D B:HEM601 4.3 34.1 1.0
C2C B:HEM601 4.3 29.8 1.0
C2D B:HEM601 4.3 31.4 1.0
C3C B:HEM601 4.3 29.6 1.0
C14 B:SI6602 4.3 33.9 1.0
CZ B:PHE120 4.7 36.9 1.0
C B:CYS443 4.9 22.2 1.0
N B:GLY445 4.9 22.8 1.0

Iron binding site 3 out of 4 in 4xrz

Go back to Iron Binding Sites List in 4xrz
Iron binding site 3 out of 4 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 6 Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Human Cytochrome P450 2D6 BACE1 Inhibitor 6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe601

b:25.1
occ:1.00
FE C:HEM601 0.0 25.1 1.0
N4 C:SI6602 2.0 26.4 1.0
NB C:HEM601 2.0 34.0 1.0
NA C:HEM601 2.0 24.7 1.0
ND C:HEM601 2.1 34.6 1.0
NC C:HEM601 2.1 26.2 1.0
SG C:CYS443 2.3 25.2 1.0
N3 C:SI6602 3.0 33.6 1.0
C4A C:HEM601 3.0 26.9 1.0
C1B C:HEM601 3.0 24.5 1.0
C16 C:SI6602 3.0 30.4 1.0
C4B C:HEM601 3.1 29.2 1.0
C1A C:HEM601 3.1 30.2 1.0
C1C C:HEM601 3.1 33.1 1.0
C4D C:HEM601 3.1 28.7 1.0
C1D C:HEM601 3.1 28.6 1.0
C4C C:HEM601 3.1 32.0 1.0
CB C:CYS443 3.2 26.9 1.0
CHB C:HEM601 3.4 33.8 1.0
CHC C:HEM601 3.4 31.5 1.0
CHA C:HEM601 3.4 30.0 1.0
CHD C:HEM601 3.5 31.3 1.0
CA C:CYS443 4.1 32.9 1.0
C15 C:SI6602 4.2 28.8 1.0
C14 C:SI6602 4.3 31.6 1.0
C3A C:HEM601 4.3 31.1 1.0
C2A C:HEM601 4.3 27.4 1.0
C2B C:HEM601 4.3 31.4 1.0
C3B C:HEM601 4.3 29.9 1.0
C2C C:HEM601 4.3 28.1 1.0
C3D C:HEM601 4.3 31.6 1.0
C2D C:HEM601 4.3 32.1 1.0
C3C C:HEM601 4.3 31.4 1.0
N C:GLY445 4.9 32.8 1.0
CZ C:PHE120 4.9 41.3 1.0
C C:CYS443 4.9 27.6 1.0

Iron binding site 4 out of 4 in 4xrz

Go back to Iron Binding Sites List in 4xrz
Iron binding site 4 out of 4 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 6 Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Human Cytochrome P450 2D6 BACE1 Inhibitor 6 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe601

b:24.5
occ:1.00
FE D:HEM601 0.0 24.5 1.0
N4 D:SI6602 2.0 26.9 1.0
NA D:HEM601 2.0 26.4 1.0
ND D:HEM601 2.0 30.5 1.0
NB D:HEM601 2.0 32.3 1.0
NC D:HEM601 2.1 30.0 1.0
SG D:CYS443 2.2 23.3 1.0
N3 D:SI6602 3.0 33.4 1.0
C4A D:HEM601 3.0 26.3 1.0
C1A D:HEM601 3.0 33.2 1.0
C16 D:SI6602 3.0 27.7 1.0
C4D D:HEM601 3.1 26.4 1.0
C1B D:HEM601 3.1 27.4 1.0
C4B D:HEM601 3.1 28.6 1.0
C1D D:HEM601 3.1 24.8 1.0
C1C D:HEM601 3.1 32.5 1.0
C4C D:HEM601 3.1 30.5 1.0
CB D:CYS443 3.2 23.6 1.0
CHB D:HEM601 3.4 27.5 1.0
CHA D:HEM601 3.4 30.3 1.0
CHC D:HEM601 3.4 30.1 1.0
CHD D:HEM601 3.5 30.4 1.0
CA D:CYS443 4.1 31.9 1.0
C15 D:SI6602 4.2 29.0 1.0
C14 D:SI6602 4.2 29.8 1.0
C3A D:HEM601 4.2 28.3 1.0
C2A D:HEM601 4.2 28.5 1.0
C3D D:HEM601 4.3 29.5 1.0
C2D D:HEM601 4.3 32.3 1.0
C2B D:HEM601 4.3 29.9 1.0
C3B D:HEM601 4.3 34.2 1.0
C2C D:HEM601 4.3 32.3 1.0
C3C D:HEM601 4.3 35.7 1.0
C D:CYS443 4.9 26.4 1.0
N D:GLY445 4.9 28.3 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: Mon Aug 5 16:00:52 2024

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