Iron in PDB 5tfu: Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex
Enzymatic activity of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex
All present enzymatic activity of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex:
1.14.14.1;
Protein crystallography data
The structure of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex, PDB code: 5tfu
was solved by
M.H.Hsu,
E.F.Johnson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.07 /
2.75
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.105,
191.756,
246.838,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.2 /
25
|
Other elements in 5tfu:
The structure of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex
(pdb code 5tfu). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex, PDB code: 5tfu:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 5tfu
Go back to
Iron Binding Sites List in 5tfu
Iron binding site 1 out
of 4 in the Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe601
b:27.4
occ:1.00
|
FE
|
A:HEM601
|
0.0
|
27.4
|
1.0
|
NB
|
A:HEM601
|
2.0
|
30.4
|
1.0
|
NA
|
A:HEM601
|
2.0
|
27.0
|
1.0
|
NC
|
A:HEM601
|
2.1
|
30.8
|
1.0
|
ND
|
A:HEM601
|
2.1
|
29.0
|
1.0
|
SG
|
A:CYS443
|
2.3
|
21.3
|
1.0
|
C4B
|
A:HEM601
|
3.1
|
32.8
|
1.0
|
C1B
|
A:HEM601
|
3.1
|
31.3
|
1.0
|
C1C
|
A:HEM601
|
3.1
|
30.3
|
1.0
|
C4A
|
A:HEM601
|
3.1
|
26.1
|
1.0
|
C1A
|
A:HEM601
|
3.1
|
27.6
|
1.0
|
C4C
|
A:HEM601
|
3.1
|
29.1
|
1.0
|
C4D
|
A:HEM601
|
3.1
|
27.8
|
1.0
|
C1D
|
A:HEM601
|
3.1
|
28.3
|
1.0
|
CB
|
A:CYS443
|
3.4
|
25.2
|
1.0
|
CHC
|
A:HEM601
|
3.4
|
31.9
|
1.0
|
CHB
|
A:HEM601
|
3.4
|
27.5
|
1.0
|
CHA
|
A:HEM601
|
3.4
|
30.9
|
1.0
|
CHD
|
A:HEM601
|
3.5
|
28.2
|
1.0
|
CA
|
A:CYS443
|
4.2
|
23.0
|
1.0
|
C2C
|
A:HEM601
|
4.3
|
31.3
|
1.0
|
C3C
|
A:HEM601
|
4.3
|
35.4
|
1.0
|
C2B
|
A:HEM601
|
4.3
|
26.2
|
1.0
|
C2A
|
A:HEM601
|
4.3
|
29.2
|
1.0
|
C3A
|
A:HEM601
|
4.3
|
25.1
|
1.0
|
C3B
|
A:HEM601
|
4.3
|
28.4
|
1.0
|
C3D
|
A:HEM601
|
4.3
|
30.5
|
1.0
|
C2D
|
A:HEM601
|
4.3
|
29.5
|
1.0
|
CB
|
A:ALA305
|
4.9
|
37.8
|
1.0
|
C
|
A:CYS443
|
5.0
|
26.6
|
1.0
|
N
|
A:GLY445
|
5.0
|
25.2
|
1.0
|
|
Iron binding site 2 out
of 4 in 5tfu
Go back to
Iron Binding Sites List in 5tfu
Iron binding site 2 out
of 4 in the Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe601
b:26.1
occ:1.00
|
FE
|
B:HEM601
|
0.0
|
26.1
|
1.0
|
NB
|
B:HEM601
|
2.0
|
30.7
|
1.0
|
NA
|
B:HEM601
|
2.0
|
25.2
|
1.0
|
NC
|
B:HEM601
|
2.1
|
40.0
|
1.0
|
ND
|
B:HEM601
|
2.1
|
32.0
|
1.0
|
SG
|
B:CYS443
|
2.3
|
28.6
|
1.0
|
C4B
|
B:HEM601
|
3.0
|
30.8
|
1.0
|
C1C
|
B:HEM601
|
3.0
|
36.9
|
1.0
|
C1B
|
B:HEM601
|
3.1
|
32.6
|
1.0
|
C4C
|
B:HEM601
|
3.1
|
38.8
|
1.0
|
C1A
|
B:HEM601
|
3.1
|
25.3
|
1.0
|
C4A
|
B:HEM601
|
3.1
|
34.3
|
1.0
|
C4D
|
B:HEM601
|
3.1
|
33.0
|
1.0
|
C1D
|
B:HEM601
|
3.1
|
26.1
|
1.0
|
CB
|
B:CYS443
|
3.3
|
25.3
|
1.0
|
CHC
|
B:HEM601
|
3.4
|
28.3
|
1.0
|
CHB
|
B:HEM601
|
3.4
|
30.5
|
1.0
|
CHA
|
B:HEM601
|
3.4
|
32.8
|
1.0
|
CHD
|
B:HEM601
|
3.4
|
38.8
|
1.0
|
CA
|
B:CYS443
|
4.1
|
28.9
|
1.0
|
C2C
|
B:HEM601
|
4.3
|
31.2
|
1.0
|
C3C
|
B:HEM601
|
4.3
|
35.5
|
1.0
|
C2B
|
B:HEM601
|
4.3
|
31.5
|
1.0
|
C3B
|
B:HEM601
|
4.3
|
34.7
|
1.0
|
C2A
|
B:HEM601
|
4.3
|
32.8
|
1.0
|
C3A
|
B:HEM601
|
4.3
|
29.0
|
1.0
|
C3D
|
B:HEM601
|
4.3
|
36.8
|
1.0
|
C2D
|
B:HEM601
|
4.3
|
37.9
|
1.0
|
C
|
B:CYS443
|
4.9
|
29.1
|
1.0
|
|
Iron binding site 3 out
of 4 in 5tfu
Go back to
Iron Binding Sites List in 5tfu
Iron binding site 3 out
of 4 in the Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe601
b:28.2
occ:1.00
|
FE
|
C:HEM601
|
0.0
|
28.2
|
1.0
|
NA
|
C:HEM601
|
2.0
|
26.7
|
1.0
|
NB
|
C:HEM601
|
2.0
|
37.4
|
1.0
|
ND
|
C:HEM601
|
2.1
|
37.9
|
1.0
|
NC
|
C:HEM601
|
2.1
|
34.4
|
1.0
|
SG
|
C:CYS443
|
2.3
|
26.9
|
1.0
|
C1A
|
C:HEM601
|
3.0
|
29.0
|
1.0
|
C1C
|
C:HEM601
|
3.1
|
38.5
|
1.0
|
C4A
|
C:HEM601
|
3.1
|
33.6
|
1.0
|
C4B
|
C:HEM601
|
3.1
|
33.0
|
1.0
|
C4C
|
C:HEM601
|
3.1
|
35.9
|
1.0
|
C1B
|
C:HEM601
|
3.1
|
32.8
|
1.0
|
C4D
|
C:HEM601
|
3.1
|
31.6
|
1.0
|
C1D
|
C:HEM601
|
3.1
|
32.7
|
1.0
|
CB
|
C:CYS443
|
3.2
|
31.2
|
1.0
|
CHA
|
C:HEM601
|
3.4
|
32.4
|
1.0
|
CHC
|
C:HEM601
|
3.4
|
36.2
|
1.0
|
CHB
|
C:HEM601
|
3.4
|
34.1
|
1.0
|
CHD
|
C:HEM601
|
3.5
|
38.3
|
1.0
|
CA
|
C:CYS443
|
4.0
|
32.6
|
1.0
|
C2A
|
C:HEM601
|
4.3
|
34.6
|
1.0
|
C2C
|
C:HEM601
|
4.3
|
37.8
|
1.0
|
C3A
|
C:HEM601
|
4.3
|
27.3
|
1.0
|
C3C
|
C:HEM601
|
4.3
|
39.7
|
1.0
|
C3B
|
C:HEM601
|
4.3
|
33.6
|
1.0
|
C2B
|
C:HEM601
|
4.3
|
33.1
|
1.0
|
C3D
|
C:HEM601
|
4.3
|
34.0
|
1.0
|
C2D
|
C:HEM601
|
4.3
|
38.1
|
1.0
|
CB
|
C:ALA305
|
4.9
|
40.4
|
1.0
|
C
|
C:CYS443
|
4.9
|
34.5
|
1.0
|
|
Iron binding site 4 out
of 4 in 5tfu
Go back to
Iron Binding Sites List in 5tfu
Iron binding site 4 out
of 4 in the Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe601
b:30.6
occ:1.00
|
FE
|
D:HEM601
|
0.0
|
30.6
|
1.0
|
NA
|
D:HEM601
|
2.0
|
34.6
|
1.0
|
NB
|
D:HEM601
|
2.0
|
39.1
|
1.0
|
ND
|
D:HEM601
|
2.1
|
42.7
|
1.0
|
NC
|
D:HEM601
|
2.1
|
36.1
|
1.0
|
SG
|
D:CYS443
|
2.3
|
27.5
|
1.0
|
C1C
|
D:HEM601
|
3.1
|
39.5
|
1.0
|
C1A
|
D:HEM601
|
3.1
|
31.0
|
1.0
|
C4B
|
D:HEM601
|
3.1
|
37.5
|
1.0
|
C4C
|
D:HEM601
|
3.1
|
38.1
|
1.0
|
C1B
|
D:HEM601
|
3.1
|
37.9
|
1.0
|
C4A
|
D:HEM601
|
3.1
|
33.2
|
1.0
|
C4D
|
D:HEM601
|
3.1
|
35.6
|
1.0
|
C1D
|
D:HEM601
|
3.1
|
31.9
|
1.0
|
CB
|
D:CYS443
|
3.3
|
31.5
|
1.0
|
CHC
|
D:HEM601
|
3.4
|
41.1
|
1.0
|
CHA
|
D:HEM601
|
3.4
|
32.8
|
1.0
|
CHB
|
D:HEM601
|
3.4
|
33.0
|
1.0
|
CHD
|
D:HEM601
|
3.4
|
35.4
|
1.0
|
CA
|
D:CYS443
|
4.1
|
34.5
|
1.0
|
C2C
|
D:HEM601
|
4.3
|
44.7
|
1.0
|
C3C
|
D:HEM601
|
4.3
|
49.5
|
1.0
|
C2A
|
D:HEM601
|
4.3
|
33.3
|
1.0
|
C3A
|
D:HEM601
|
4.3
|
32.9
|
1.0
|
C2B
|
D:HEM601
|
4.3
|
35.8
|
1.0
|
C3B
|
D:HEM601
|
4.3
|
36.5
|
1.0
|
C3D
|
D:HEM601
|
4.3
|
37.9
|
1.0
|
C2D
|
D:HEM601
|
4.3
|
39.4
|
1.0
|
CB
|
D:ALA305
|
4.9
|
36.5
|
1.0
|
O
|
D:ALA305
|
4.9
|
54.0
|
1.0
|
C
|
D:CYS443
|
5.0
|
36.1
|
1.0
|
CG2
|
D:THR309
|
5.0
|
38.9
|
1.0
|
|
Reference:
C.R.Butler,
K.Ogilvie,
L.Martinez-Alsina,
G.Barreiro,
E.M.Beck,
C.E.Nolan,
K.Atchison,
E.Benvenuti,
L.Buzon,
S.Doran,
C.Gonzales,
C.J.Helal,
X.Hou,
M.H.Hsu,
E.F.Johnson,
K.Lapham,
L.Lanyon,
K.Parris,
B.T.O'neill,
D.Riddell,
A.Robshaw,
F.Vajdos,
M.A.Brodney.
Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality. J. Med. Chem. V. 60 386 2017.
ISSN: ISSN 1520-4804
PubMed: 27997172
DOI: 10.1021/ACS.JMEDCHEM.6B01451
Page generated: Tue Aug 6 08:58:06 2024
|