Iron 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 Binding Sites:
The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron where determined in the
Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex, PDB code: 4xry:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 4xry
Go back to
Iron Binding Sites List in 4xry
Iron binding site 1 out
of 4 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 5 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 5 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe601
b:28.3
occ:1.00
|
FE
|
A:HEM601
|
0.0
|
28.3
|
1.0
|
NB
|
A:HEM601
|
2.1
|
38.0
|
1.0
|
ND
|
A:HEM601
|
2.1
|
33.2
|
1.0
|
NC
|
A:HEM601
|
2.1
|
36.4
|
1.0
|
NA
|
A:HEM601
|
2.1
|
28.1
|
1.0
|
SG
|
A:CYS443
|
2.2
|
27.9
|
1.0
|
C4C
|
A:HEM601
|
3.0
|
33.6
|
1.0
|
C1C
|
A:HEM601
|
3.1
|
29.2
|
1.0
|
C1B
|
A:HEM601
|
3.1
|
27.3
|
1.0
|
C4A
|
A:HEM601
|
3.1
|
26.5
|
1.0
|
C1D
|
A:HEM601
|
3.1
|
27.8
|
1.0
|
C4B
|
A:HEM601
|
3.1
|
36.6
|
1.0
|
C1A
|
A:HEM601
|
3.1
|
28.6
|
1.0
|
C4D
|
A:HEM601
|
3.1
|
28.3
|
1.0
|
CB
|
A:CYS443
|
3.4
|
28.8
|
1.0
|
CHD
|
A:HEM601
|
3.4
|
29.6
|
1.0
|
CHB
|
A:HEM601
|
3.4
|
28.5
|
1.0
|
CHC
|
A:HEM601
|
3.4
|
36.8
|
1.0
|
CHA
|
A:HEM601
|
3.5
|
27.1
|
1.0
|
CA
|
A:CYS443
|
4.1
|
28.4
|
1.0
|
C17
|
A:SI5602
|
4.2
|
47.9
|
1.0
|
C3C
|
A:HEM601
|
4.3
|
39.0
|
1.0
|
C2C
|
A:HEM601
|
4.3
|
38.6
|
1.0
|
C3A
|
A:HEM601
|
4.3
|
38.0
|
1.0
|
C2B
|
A:HEM601
|
4.3
|
34.3
|
1.0
|
C2A
|
A:HEM601
|
4.3
|
33.4
|
1.0
|
C2D
|
A:HEM601
|
4.3
|
25.8
|
1.0
|
C3B
|
A:HEM601
|
4.3
|
34.4
|
1.0
|
C3D
|
A:HEM601
|
4.3
|
33.6
|
1.0
|
O
|
A:ALA305
|
4.5
|
53.0
|
1.0
|
C
|
A:CYS443
|
4.9
|
24.9
|
1.0
|
N
|
A:GLY445
|
5.0
|
27.8
|
1.0
|
CB
|
A:ALA305
|
5.0
|
50.3
|
1.0
|
|
Iron binding site 2 out
of 4 in 4xry
Go back to
Iron Binding Sites List in 4xry
Iron binding site 2 out
of 4 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 5 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 5 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe601
b:25.4
occ:1.00
|
FE
|
B:HEM601
|
0.0
|
25.4
|
1.0
|
O
|
B:HOH726
|
2.0
|
29.1
|
1.0
|
NC
|
B:HEM601
|
2.1
|
37.9
|
1.0
|
NB
|
B:HEM601
|
2.1
|
32.5
|
1.0
|
ND
|
B:HEM601
|
2.1
|
30.6
|
1.0
|
NA
|
B:HEM601
|
2.1
|
25.9
|
1.0
|
SG
|
B:CYS443
|
2.2
|
26.9
|
1.0
|
C4C
|
B:HEM601
|
3.0
|
39.8
|
1.0
|
C1C
|
B:HEM601
|
3.0
|
41.8
|
1.0
|
C4B
|
B:HEM601
|
3.1
|
34.9
|
1.0
|
C1D
|
B:HEM601
|
3.1
|
32.6
|
1.0
|
C1B
|
B:HEM601
|
3.1
|
31.5
|
1.0
|
C4A
|
B:HEM601
|
3.1
|
27.5
|
1.0
|
C4D
|
B:HEM601
|
3.1
|
30.1
|
1.0
|
C1A
|
B:HEM601
|
3.1
|
31.8
|
1.0
|
CB
|
B:CYS443
|
3.2
|
28.7
|
1.0
|
CHD
|
B:HEM601
|
3.4
|
31.9
|
1.0
|
CHC
|
B:HEM601
|
3.4
|
31.0
|
1.0
|
CHB
|
B:HEM601
|
3.4
|
33.7
|
1.0
|
CHA
|
B:HEM601
|
3.5
|
29.7
|
1.0
|
CA
|
B:CYS443
|
4.0
|
31.5
|
1.0
|
C3C
|
B:HEM601
|
4.2
|
43.3
|
1.0
|
C2C
|
B:HEM601
|
4.2
|
38.0
|
1.0
|
C3B
|
B:HEM601
|
4.3
|
32.3
|
1.0
|
C2B
|
B:HEM601
|
4.3
|
37.5
|
1.0
|
C2D
|
B:HEM601
|
4.3
|
32.7
|
1.0
|
C3D
|
B:HEM601
|
4.3
|
34.5
|
1.0
|
C3A
|
B:HEM601
|
4.3
|
35.2
|
1.0
|
C2A
|
B:HEM601
|
4.3
|
34.3
|
1.0
|
C17
|
B:SI5602
|
4.6
|
39.4
|
1.0
|
C
|
B:CYS443
|
4.8
|
28.9
|
1.0
|
N
|
B:GLY445
|
4.8
|
31.2
|
1.0
|
N
|
B:LEU444
|
4.9
|
27.4
|
1.0
|
|
Iron binding site 3 out
of 4 in 4xry
Go back to
Iron Binding Sites List in 4xry
Iron binding site 3 out
of 4 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 5 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 5 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe601
b:31.7
occ:1.00
|
FE
|
C:HEM601
|
0.0
|
31.7
|
1.0
|
ND
|
C:HEM601
|
2.0
|
44.2
|
1.0
|
NA
|
C:HEM601
|
2.1
|
39.1
|
1.0
|
NC
|
C:HEM601
|
2.1
|
43.8
|
1.0
|
NB
|
C:HEM601
|
2.1
|
39.5
|
1.0
|
SG
|
C:CYS443
|
2.2
|
27.9
|
1.0
|
C1D
|
C:HEM601
|
3.0
|
30.5
|
1.0
|
C4C
|
C:HEM601
|
3.0
|
39.9
|
1.0
|
C4D
|
C:HEM601
|
3.1
|
34.9
|
1.0
|
C4A
|
C:HEM601
|
3.1
|
27.1
|
1.0
|
C1A
|
C:HEM601
|
3.1
|
36.2
|
1.0
|
C1B
|
C:HEM601
|
3.1
|
33.2
|
1.0
|
C1C
|
C:HEM601
|
3.1
|
42.0
|
1.0
|
C4B
|
C:HEM601
|
3.1
|
46.5
|
1.0
|
CB
|
C:CYS443
|
3.4
|
27.5
|
1.0
|
CHD
|
C:HEM601
|
3.4
|
34.1
|
1.0
|
CHB
|
C:HEM601
|
3.4
|
36.9
|
1.0
|
CHA
|
C:HEM601
|
3.4
|
36.9
|
1.0
|
CHC
|
C:HEM601
|
3.5
|
40.9
|
1.0
|
CA
|
C:CYS443
|
4.1
|
39.3
|
1.0
|
C2D
|
C:HEM601
|
4.3
|
29.0
|
1.0
|
C3C
|
C:HEM601
|
4.3
|
45.6
|
1.0
|
C3D
|
C:HEM601
|
4.3
|
38.5
|
1.0
|
C2C
|
C:HEM601
|
4.3
|
45.0
|
1.0
|
C3A
|
C:HEM601
|
4.3
|
41.2
|
1.0
|
C2A
|
C:HEM601
|
4.3
|
37.5
|
1.0
|
C2B
|
C:HEM601
|
4.3
|
39.5
|
1.0
|
C3B
|
C:HEM601
|
4.3
|
38.1
|
1.0
|
C17
|
C:SI5602
|
4.4
|
48.8
|
1.0
|
O
|
C:ALA305
|
4.7
|
64.0
|
1.0
|
OG1
|
C:THR309
|
4.9
|
44.4
|
1.0
|
C
|
C:CYS443
|
4.9
|
37.2
|
1.0
|
|
Iron binding site 4 out
of 4 in 4xry
Go back to
Iron Binding Sites List in 4xry
Iron binding site 4 out
of 4 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 5 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 5 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe601
b:33.6
occ:1.00
|
FE
|
D:HEM601
|
0.0
|
33.6
|
1.0
|
NB
|
D:HEM601
|
2.0
|
45.5
|
1.0
|
ND
|
D:HEM601
|
2.1
|
41.3
|
1.0
|
NA
|
D:HEM601
|
2.1
|
37.0
|
1.0
|
NC
|
D:HEM601
|
2.1
|
43.8
|
1.0
|
O
|
D:HOH721
|
2.1
|
36.4
|
1.0
|
SG
|
D:CYS443
|
2.2
|
32.1
|
1.0
|
C4C
|
D:HEM601
|
3.0
|
44.7
|
1.0
|
C1B
|
D:HEM601
|
3.1
|
40.3
|
1.0
|
C1D
|
D:HEM601
|
3.1
|
32.7
|
1.0
|
C4A
|
D:HEM601
|
3.1
|
35.7
|
1.0
|
C1C
|
D:HEM601
|
3.1
|
43.8
|
1.0
|
C4B
|
D:HEM601
|
3.1
|
44.5
|
1.0
|
C4D
|
D:HEM601
|
3.1
|
36.5
|
1.0
|
C1A
|
D:HEM601
|
3.1
|
39.7
|
1.0
|
CB
|
D:CYS443
|
3.2
|
31.9
|
1.0
|
CHB
|
D:HEM601
|
3.4
|
40.2
|
1.0
|
CHD
|
D:HEM601
|
3.4
|
40.0
|
1.0
|
CHC
|
D:HEM601
|
3.5
|
53.0
|
1.0
|
CHA
|
D:HEM601
|
3.5
|
36.8
|
1.0
|
CA
|
D:CYS443
|
4.0
|
36.1
|
1.0
|
C3C
|
D:HEM601
|
4.2
|
52.5
|
1.0
|
C2C
|
D:HEM601
|
4.3
|
51.3
|
1.0
|
C2B
|
D:HEM601
|
4.3
|
44.5
|
1.0
|
C2D
|
D:HEM601
|
4.3
|
31.7
|
1.0
|
C3A
|
D:HEM601
|
4.3
|
43.7
|
1.0
|
C3B
|
D:HEM601
|
4.3
|
41.4
|
1.0
|
C3D
|
D:HEM601
|
4.3
|
41.4
|
1.0
|
C2A
|
D:HEM601
|
4.3
|
38.8
|
1.0
|
C17
|
D:SI5602
|
4.5
|
48.1
|
1.0
|
O
|
D:ALA305
|
4.6
|
66.0
|
1.0
|
C
|
D:CYS443
|
4.8
|
37.6
|
1.0
|
N
|
D:GLY445
|
4.9
|
39.5
|
1.0
|
N
|
D:LEU444
|
4.9
|
40.1
|
1.0
|
CD2
|
D:PHE436
|
5.0
|
38.5
|
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
|