Zinc 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:
Zinc Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
17;
Binding sites:
The binding sites of Zinc 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 Zinc atom.
In total 17 binding sites of Zinc where determined in the
Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex, PDB code: 4xry:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Zinc binding site 1 out
of 17 in 4xry
Go back to
Zinc Binding Sites List in 4xry
Zinc binding site 1 out
of 17 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn 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:Zn603
b:33.5
occ:1.00
|
OE2
|
A:GLU273
|
1.9
|
28.5
|
1.0
|
OD2
|
A:ASP270
|
2.0
|
38.5
|
1.0
|
NE2
|
A:HIS258
|
2.1
|
24.8
|
1.0
|
CD
|
A:GLU273
|
2.8
|
34.5
|
1.0
|
CG
|
A:ASP270
|
2.9
|
31.6
|
1.0
|
CE1
|
A:HIS258
|
3.0
|
33.3
|
1.0
|
CD2
|
A:HIS258
|
3.1
|
28.2
|
1.0
|
OD1
|
A:ASP270
|
3.2
|
25.6
|
1.0
|
CG
|
A:GLU273
|
3.3
|
27.9
|
1.0
|
O
|
A:CYS191
|
3.6
|
40.1
|
1.0
|
OE1
|
A:GLU273
|
3.9
|
29.3
|
1.0
|
O
|
A:HOH704
|
4.2
|
37.7
|
1.0
|
ND1
|
A:HIS258
|
4.2
|
42.8
|
1.0
|
C
|
A:CYS191
|
4.2
|
33.7
|
1.0
|
CG
|
A:HIS258
|
4.2
|
26.3
|
1.0
|
CB
|
A:ASP270
|
4.3
|
24.5
|
1.0
|
NH2
|
A:ARG269
|
4.4
|
37.4
|
1.0
|
NE
|
A:ARG269
|
4.6
|
51.3
|
1.0
|
CB
|
A:GLU273
|
4.6
|
29.5
|
1.0
|
CA
|
A:GLY192
|
4.7
|
35.2
|
1.0
|
CB
|
A:ARG269
|
4.7
|
40.9
|
1.0
|
N
|
A:GLY192
|
4.7
|
41.3
|
1.0
|
N
|
A:ASP270
|
4.9
|
33.5
|
1.0
|
CA
|
A:CYS191
|
4.9
|
33.3
|
1.0
|
CZ
|
A:ARG269
|
5.0
|
38.2
|
1.0
|
|
Zinc binding site 2 out
of 17 in 4xry
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Zinc Binding Sites List in 4xry
Zinc binding site 2 out
of 17 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn604
b:69.7
occ:1.00
|
SG
|
A:CYS191
|
2.4
|
64.2
|
1.0
|
CB
|
A:CYS191
|
2.9
|
50.5
|
1.0
|
CA
|
A:CYS191
|
4.2
|
33.3
|
1.0
|
OG1
|
A:THR190
|
4.2
|
54.1
|
1.0
|
N
|
A:CYS191
|
4.3
|
36.3
|
1.0
|
CB
|
A:LEU254
|
4.7
|
29.6
|
1.0
|
CB
|
A:ALA187
|
4.7
|
34.4
|
1.0
|
O
|
A:ALA187
|
4.7
|
35.0
|
1.0
|
CZ
|
A:PHE195
|
4.7
|
34.1
|
1.0
|
CA
|
A:ALA187
|
4.8
|
37.6
|
1.0
|
CE1
|
A:PHE195
|
4.9
|
30.4
|
1.0
|
CB
|
A:THR190
|
5.0
|
39.0
|
1.0
|
|
Zinc binding site 3 out
of 17 in 4xry
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Zinc Binding Sites List in 4xry
Zinc binding site 3 out
of 17 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn605
b:75.1
occ:1.00
|
ND1
|
A:HIS463
|
1.9
|
64.2
|
1.0
|
O
|
A:HOH736
|
2.1
|
45.2
|
1.0
|
O
|
A:HOH734
|
2.2
|
65.7
|
1.0
|
CE1
|
A:HIS463
|
2.9
|
67.2
|
1.0
|
CG
|
A:HIS463
|
2.9
|
57.6
|
1.0
|
CB
|
A:HIS463
|
3.3
|
43.4
|
1.0
|
CA
|
A:HIS463
|
3.8
|
52.9
|
1.0
|
NE2
|
A:HIS463
|
4.0
|
70.7
|
1.0
|
CD2
|
A:HIS463
|
4.0
|
61.1
|
1.0
|
O
|
A:HIS463
|
4.2
|
59.2
|
1.0
|
C
|
A:HIS463
|
4.5
|
54.3
|
1.0
|
C
|
A:ARG497
|
4.7
|
74.3
|
1.0
|
O
|
A:GLN341
|
4.8
|
82.4
|
1.0
|
N
|
A:ARG497
|
4.9
|
72.1
|
1.0
|
O
|
A:HOH708
|
5.0
|
51.4
|
1.0
|
|
Zinc binding site 4 out
of 17 in 4xry
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Zinc Binding Sites List in 4xry
Zinc binding site 4 out
of 17 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn606
b:46.5
occ:1.00
|
OD2
|
A:ASP422
|
2.0
|
43.3
|
1.0
|
OD2
|
B:ASP422
|
2.0
|
43.4
|
1.0
|
ND1
|
A:HIS426
|
2.0
|
55.1
|
1.0
|
ND1
|
B:HIS426
|
2.0
|
50.1
|
1.0
|
CE1
|
A:HIS426
|
2.9
|
61.0
|
1.0
|
CG
|
B:ASP422
|
3.0
|
38.7
|
1.0
|
CG
|
B:HIS426
|
3.0
|
53.1
|
1.0
|
CE1
|
B:HIS426
|
3.0
|
55.2
|
1.0
|
CG
|
A:HIS426
|
3.0
|
59.9
|
1.0
|
CG
|
A:ASP422
|
3.1
|
40.7
|
1.0
|
CB
|
B:HIS426
|
3.3
|
42.0
|
1.0
|
OD1
|
B:ASP422
|
3.4
|
40.5
|
1.0
|
CB
|
A:HIS426
|
3.4
|
39.0
|
1.0
|
OD1
|
A:ASP422
|
3.5
|
42.9
|
1.0
|
CB
|
B:GLN424
|
4.0
|
52.3
|
1.0
|
CB
|
A:GLN424
|
4.0
|
55.8
|
1.0
|
NE2
|
A:HIS426
|
4.0
|
68.7
|
1.0
|
NE2
|
B:HIS426
|
4.1
|
63.4
|
1.0
|
CD2
|
B:HIS426
|
4.1
|
46.2
|
1.0
|
CD2
|
A:HIS426
|
4.1
|
49.5
|
1.0
|
CB
|
B:ASP422
|
4.2
|
36.3
|
1.0
|
CB
|
A:ASP422
|
4.3
|
40.1
|
1.0
|
CA
|
B:HIS426
|
4.6
|
46.0
|
1.0
|
CG
|
A:GLN424
|
4.6
|
63.4
|
1.0
|
N
|
B:HIS426
|
4.6
|
40.8
|
1.0
|
CG
|
B:GLN424
|
4.6
|
58.4
|
1.0
|
CA
|
A:HIS426
|
4.7
|
48.6
|
1.0
|
N
|
A:HIS426
|
4.8
|
44.3
|
1.0
|
|
Zinc binding site 5 out
of 17 in 4xry
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Zinc Binding Sites List in 4xry
Zinc binding site 5 out
of 17 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn603
b:36.4
occ:1.00
|
OE2
|
B:GLU273
|
1.9
|
29.3
|
1.0
|
NE2
|
B:HIS258
|
2.0
|
30.0
|
1.0
|
OD2
|
B:ASP270
|
2.0
|
44.7
|
1.0
|
CD
|
B:GLU273
|
2.8
|
36.6
|
1.0
|
CE1
|
B:HIS258
|
2.9
|
33.3
|
1.0
|
CG
|
B:ASP270
|
2.9
|
33.2
|
1.0
|
CD2
|
B:HIS258
|
3.1
|
36.1
|
1.0
|
OD1
|
B:ASP270
|
3.1
|
31.7
|
1.0
|
CG
|
B:GLU273
|
3.3
|
33.6
|
1.0
|
O
|
B:CYS191
|
3.5
|
43.7
|
1.0
|
OE1
|
B:GLU273
|
3.9
|
38.5
|
1.0
|
O
|
B:HOH701
|
3.9
|
32.7
|
1.0
|
ND1
|
B:HIS258
|
4.1
|
39.7
|
1.0
|
CG
|
B:HIS258
|
4.2
|
26.5
|
1.0
|
C
|
B:CYS191
|
4.2
|
37.3
|
1.0
|
O
|
B:HOH708
|
4.3
|
46.2
|
1.0
|
CB
|
B:ASP270
|
4.3
|
26.3
|
1.0
|
NH2
|
B:ARG269
|
4.4
|
35.7
|
1.0
|
NE
|
B:ARG269
|
4.5
|
55.0
|
1.0
|
CA
|
B:GLY192
|
4.6
|
37.7
|
1.0
|
CB
|
B:GLU273
|
4.6
|
34.3
|
1.0
|
CB
|
B:ARG269
|
4.6
|
39.2
|
1.0
|
N
|
B:GLY192
|
4.7
|
38.0
|
1.0
|
CZ
|
B:ARG269
|
4.9
|
44.4
|
1.0
|
N
|
B:ASP270
|
4.9
|
37.9
|
1.0
|
|
Zinc binding site 6 out
of 17 in 4xry
Go back to
Zinc Binding Sites List in 4xry
Zinc binding site 6 out
of 17 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn604
b:70.3
occ:1.00
|
SG
|
B:CYS191
|
2.4
|
71.3
|
1.0
|
CB
|
B:CYS191
|
2.9
|
45.9
|
1.0
|
OG1
|
B:THR190
|
4.3
|
48.7
|
1.0
|
CA
|
B:CYS191
|
4.3
|
38.3
|
1.0
|
CB
|
B:LEU254
|
4.4
|
26.8
|
1.0
|
CE1
|
B:PHE303
|
4.5
|
64.8
|
1.0
|
N
|
B:CYS191
|
4.5
|
37.1
|
1.0
|
CD1
|
B:LEU254
|
4.6
|
39.1
|
1.0
|
CB
|
B:ALA187
|
4.8
|
26.5
|
1.0
|
CZ
|
B:PHE195
|
4.8
|
34.4
|
1.0
|
CA
|
B:ALA187
|
4.8
|
35.4
|
1.0
|
O
|
B:ALA187
|
4.8
|
31.6
|
1.0
|
CD1
|
B:PHE303
|
4.9
|
58.4
|
1.0
|
CE1
|
B:PHE195
|
4.9
|
31.1
|
1.0
|
|
Zinc binding site 7 out
of 17 in 4xry
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Zinc Binding Sites List in 4xry
Zinc binding site 7 out
of 17 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn605
b:76.9
occ:1.00
|
ND1
|
B:HIS463
|
2.0
|
54.0
|
1.0
|
O
|
B:HOH730
|
2.1
|
55.3
|
1.0
|
CG
|
B:HIS463
|
2.9
|
53.6
|
1.0
|
CE1
|
B:HIS463
|
3.0
|
64.0
|
1.0
|
CB
|
B:HIS463
|
3.2
|
41.9
|
1.0
|
CA
|
B:HIS463
|
3.7
|
51.4
|
1.0
|
O
|
B:HIS463
|
4.0
|
51.6
|
1.0
|
CD2
|
B:HIS463
|
4.0
|
58.9
|
1.0
|
NE2
|
B:HIS463
|
4.1
|
61.1
|
1.0
|
OE1
|
B:GLN341
|
4.2
|
81.5
|
1.0
|
O
|
B:ARG497
|
4.3
|
75.6
|
1.0
|
C
|
B:HIS463
|
4.3
|
49.8
|
1.0
|
N
|
B:ARG497
|
4.8
|
66.6
|
1.0
|
O
|
B:GLN341
|
4.8
|
85.1
|
1.0
|
O
|
B:HOH734
|
4.9
|
53.5
|
1.0
|
N
|
B:HIS463
|
5.0
|
52.1
|
1.0
|
|
Zinc binding site 8 out
of 17 in 4xry
Go back to
Zinc Binding Sites List in 4xry
Zinc binding site 8 out
of 17 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn603
b:37.2
occ:1.00
|
OE2
|
C:GLU273
|
2.0
|
27.0
|
1.0
|
NE2
|
C:HIS258
|
2.0
|
30.4
|
1.0
|
OD2
|
C:ASP270
|
2.1
|
42.3
|
1.0
|
CD
|
C:GLU273
|
2.9
|
31.4
|
1.0
|
CE1
|
C:HIS258
|
2.9
|
31.8
|
1.0
|
CG
|
C:ASP270
|
3.0
|
35.9
|
1.0
|
CD2
|
C:HIS258
|
3.0
|
41.3
|
1.0
|
OD1
|
C:ASP270
|
3.2
|
30.4
|
1.0
|
CG
|
C:GLU273
|
3.3
|
29.8
|
1.0
|
O
|
C:CYS191
|
3.8
|
30.4
|
1.0
|
OE1
|
C:GLU273
|
3.9
|
26.7
|
1.0
|
O
|
C:HOH707
|
4.0
|
39.1
|
1.0
|
ND1
|
C:HIS258
|
4.1
|
31.0
|
1.0
|
CG
|
C:HIS258
|
4.1
|
24.2
|
1.0
|
C
|
C:CYS191
|
4.3
|
35.2
|
1.0
|
CB
|
C:ASP270
|
4.4
|
34.4
|
1.0
|
CA
|
C:GLY192
|
4.6
|
40.8
|
1.0
|
CB
|
C:GLU273
|
4.6
|
33.2
|
1.0
|
NE
|
C:ARG269
|
4.6
|
52.6
|
1.0
|
CB
|
C:ARG269
|
4.7
|
45.8
|
1.0
|
NH2
|
C:ARG269
|
4.7
|
29.8
|
1.0
|
N
|
C:GLY192
|
4.8
|
39.2
|
1.0
|
|
Zinc binding site 9 out
of 17 in 4xry
Go back to
Zinc Binding Sites List in 4xry
Zinc binding site 9 out
of 17 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 9 of Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn604
b:69.9
occ:1.00
|
SG
|
C:CYS191
|
2.2
|
75.1
|
1.0
|
CB
|
C:CYS191
|
3.1
|
50.4
|
1.0
|
CD1
|
C:LEU254
|
4.5
|
31.0
|
1.0
|
CB
|
C:LEU254
|
4.5
|
32.1
|
1.0
|
CA
|
C:CYS191
|
4.5
|
36.9
|
1.0
|
OG1
|
C:THR190
|
4.6
|
44.5
|
1.0
|
CZ
|
C:PHE195
|
4.8
|
32.7
|
1.0
|
CD1
|
C:LEU251
|
4.8
|
39.6
|
1.0
|
CE1
|
C:PHE195
|
4.8
|
23.4
|
1.0
|
O
|
C:ALA187
|
4.9
|
32.0
|
1.0
|
N
|
C:CYS191
|
4.9
|
38.7
|
1.0
|
CB
|
C:ALA187
|
4.9
|
29.6
|
1.0
|
CA
|
C:ALA187
|
5.0
|
36.4
|
1.0
|
|
Zinc binding site 10 out
of 17 in 4xry
Go back to
Zinc Binding Sites List in 4xry
Zinc binding site 10 out
of 17 in the Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 10 of Human Cytochrome P450 2D6 BACE1 Inhibitor 5 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn605
b:89.4
occ:1.00
|
NE2
|
C:HIS324
|
2.1
|
65.2
|
1.0
|
O
|
C:HOH734
|
2.2
|
34.1
|
1.0
|
CE1
|
C:HIS324
|
2.5
|
59.1
|
1.0
|
CD2
|
C:HIS324
|
3.3
|
55.6
|
1.0
|
ND1
|
C:HIS324
|
3.8
|
67.6
|
1.0
|
CG
|
C:HIS324
|
4.2
|
52.6
|
1.0
|
CB
|
C:PHE415
|
4.4
|
48.0
|
1.0
|
N
|
C:PHE415
|
4.7
|
43.0
|
1.0
|
CG
|
C:HIS477
|
4.8
|
60.0
|
1.0
|
ND1
|
C:HIS477
|
4.8
|
81.7
|
1.0
|
CD2
|
C:HIS477
|
4.9
|
79.2
|
1.0
|
CE1
|
C:HIS477
|
5.0
|
95.7
|
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: Sun Oct 27 10:44:36 2024
|