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:
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
|