Magnesium in PDB 6zqz: [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors
Enzymatic activity of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors
All present enzymatic activity of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors:
3.1.4.17;
Protein crystallography data
The structure of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors, PDB code: 6zqz
was solved by
G.Tresadern,
P.M.Leonard,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
87.07 /
1.88
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
55.960,
73.460,
92.230,
109.16,
91.37,
91.26
|
R / Rfree (%)
|
19.6 /
24.4
|
Other elements in 6zqz:
The structure of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors
(pdb code 6zqz). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
[1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors, PDB code: 6zqz:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 6zqz
Go back to
Magnesium Binding Sites List in 6zqz
Magnesium binding site 1 out
of 5 in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1002
b:11.2
occ:1.00
|
O
|
A:HOH1200
|
2.1
|
9.7
|
1.0
|
O
|
A:HOH1183
|
2.1
|
9.2
|
1.0
|
OD1
|
A:ASP697
|
2.1
|
8.7
|
1.0
|
O
|
A:HOH1141
|
2.1
|
8.4
|
1.0
|
O
|
A:HOH1165
|
2.1
|
10.0
|
1.0
|
O
|
A:HOH1214
|
2.2
|
9.3
|
1.0
|
CG
|
A:ASP697
|
3.1
|
8.9
|
1.0
|
OD2
|
A:ASP697
|
3.4
|
8.9
|
1.0
|
ZN
|
A:ZN1001
|
3.7
|
13.7
|
1.0
|
O
|
A:HOH1326
|
3.8
|
19.6
|
1.0
|
O
|
A:HOH1201
|
4.0
|
18.3
|
1.0
|
NE2
|
A:HIS730
|
4.1
|
10.0
|
1.0
|
OG1
|
A:THR768
|
4.2
|
10.1
|
1.0
|
CD2
|
A:HIS696
|
4.2
|
8.7
|
1.0
|
CD2
|
A:HIS730
|
4.3
|
9.7
|
1.0
|
O
|
A:HOH1251
|
4.3
|
10.8
|
1.0
|
O
|
A:HIS696
|
4.3
|
9.2
|
1.0
|
OE2
|
A:GLU727
|
4.4
|
11.6
|
1.0
|
NE2
|
A:HIS656
|
4.4
|
11.2
|
1.0
|
CD2
|
A:HIS700
|
4.5
|
11.2
|
1.0
|
CD2
|
A:HIS656
|
4.5
|
10.8
|
1.0
|
CB
|
A:ASP697
|
4.5
|
9.0
|
1.0
|
OD2
|
A:ASP808
|
4.6
|
12.5
|
1.0
|
NE2
|
A:HIS696
|
4.6
|
8.9
|
1.0
|
CB
|
A:THR768
|
4.6
|
10.6
|
1.0
|
O
|
A:THR768
|
4.7
|
10.9
|
1.0
|
NE2
|
A:HIS700
|
4.8
|
11.3
|
1.0
|
CA
|
A:ASP697
|
4.9
|
8.9
|
1.0
|
CG
|
A:GLU727
|
4.9
|
10.8
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 6zqz
Go back to
Magnesium Binding Sites List in 6zqz
Magnesium binding site 2 out
of 5 in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1002
b:12.3
occ:1.00
|
O
|
B:HOH1119
|
2.0
|
10.8
|
1.0
|
O
|
B:HOH1124
|
2.1
|
10.4
|
1.0
|
O
|
B:HOH1166
|
2.1
|
10.3
|
1.0
|
O
|
B:HOH1160
|
2.2
|
9.5
|
1.0
|
OD1
|
B:ASP697
|
2.2
|
9.6
|
1.0
|
O
|
B:HOH1178
|
2.2
|
11.8
|
1.0
|
CG
|
B:ASP697
|
3.2
|
10.3
|
1.0
|
OD2
|
B:ASP697
|
3.5
|
9.9
|
1.0
|
ZN
|
B:ZN1001
|
3.7
|
15.0
|
1.0
|
O
|
B:HOH1312
|
4.0
|
18.0
|
1.0
|
O
|
B:HOH1215
|
4.0
|
21.9
|
1.0
|
OG1
|
B:THR768
|
4.0
|
11.2
|
1.0
|
OE2
|
B:GLU727
|
4.1
|
16.3
|
1.0
|
NE2
|
B:HIS730
|
4.2
|
11.8
|
1.0
|
CD2
|
B:HIS696
|
4.2
|
10.2
|
1.0
|
O
|
B:HOH1287
|
4.3
|
16.9
|
1.0
|
O
|
B:HIS696
|
4.3
|
10.7
|
1.0
|
CD2
|
B:HIS730
|
4.4
|
11.9
|
1.0
|
OD2
|
B:ASP808
|
4.4
|
14.4
|
1.0
|
CB
|
B:THR768
|
4.5
|
11.4
|
1.0
|
CB
|
B:ASP697
|
4.6
|
10.5
|
1.0
|
O
|
B:THR768
|
4.6
|
12.6
|
1.0
|
NE2
|
B:HIS656
|
4.6
|
13.2
|
1.0
|
CD2
|
B:HIS656
|
4.6
|
12.9
|
1.0
|
NE2
|
B:HIS696
|
4.6
|
10.6
|
1.0
|
CD2
|
B:HIS700
|
4.7
|
13.8
|
1.0
|
CA
|
B:ASP697
|
4.9
|
11.2
|
1.0
|
CD
|
B:GLU727
|
4.9
|
15.4
|
1.0
|
CG
|
B:GLU727
|
4.9
|
15.1
|
1.0
|
NE2
|
B:HIS700
|
4.9
|
13.9
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 6zqz
Go back to
Magnesium Binding Sites List in 6zqz
Magnesium binding site 3 out
of 5 in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1004
b:27.5
occ:1.00
|
O
|
B:HOH1304
|
2.1
|
19.7
|
1.0
|
O
|
B:HOH1308
|
2.1
|
28.0
|
1.0
|
O
|
B:HOH1103
|
2.2
|
20.8
|
1.0
|
OD2
|
B:ASP789
|
4.1
|
22.7
|
1.0
|
ND2
|
B:ASN792
|
4.1
|
20.2
|
1.0
|
O
|
B:HOH1320
|
4.2
|
25.8
|
1.0
|
O
|
B:HOH1175
|
4.2
|
30.3
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 6zqz
Go back to
Magnesium Binding Sites List in 6zqz
Magnesium binding site 4 out
of 5 in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1002
b:10.2
occ:1.00
|
O
|
C:HOH1171
|
2.1
|
10.9
|
1.0
|
O
|
C:HOH1135
|
2.1
|
9.4
|
1.0
|
O
|
C:HOH1172
|
2.1
|
9.5
|
1.0
|
OD1
|
C:ASP697
|
2.1
|
10.1
|
1.0
|
O
|
C:HOH1154
|
2.1
|
9.8
|
1.0
|
O
|
C:HOH1105
|
2.2
|
12.2
|
1.0
|
CG
|
C:ASP697
|
3.2
|
11.1
|
1.0
|
OD2
|
C:ASP697
|
3.5
|
11.0
|
1.0
|
ZN
|
C:ZN1001
|
3.7
|
15.4
|
1.0
|
O
|
C:HOH1127
|
4.1
|
15.9
|
1.0
|
O
|
C:HOH1264
|
4.1
|
17.0
|
1.0
|
OE2
|
C:GLU727
|
4.1
|
15.1
|
1.0
|
O
|
C:HOH1119
|
4.1
|
13.1
|
1.0
|
NE2
|
C:HIS730
|
4.1
|
12.8
|
1.0
|
OG1
|
C:THR768
|
4.2
|
12.8
|
1.0
|
CD2
|
C:HIS696
|
4.2
|
11.1
|
1.0
|
O
|
C:HIS696
|
4.3
|
11.5
|
1.0
|
CD2
|
C:HIS730
|
4.4
|
12.8
|
1.0
|
CD2
|
C:HIS700
|
4.4
|
14.6
|
1.0
|
NE2
|
C:HIS656
|
4.5
|
13.2
|
1.0
|
CB
|
C:ASP697
|
4.5
|
11.3
|
1.0
|
OD2
|
C:ASP808
|
4.5
|
14.2
|
1.0
|
CD2
|
C:HIS656
|
4.6
|
12.7
|
1.0
|
CB
|
C:THR768
|
4.6
|
13.6
|
1.0
|
O
|
C:THR768
|
4.7
|
14.3
|
1.0
|
NE2
|
C:HIS700
|
4.7
|
13.8
|
1.0
|
NE2
|
C:HIS696
|
4.7
|
11.7
|
1.0
|
O
|
C:HOH1140
|
4.8
|
27.2
|
1.0
|
CA
|
C:ASP697
|
4.8
|
11.6
|
1.0
|
CD
|
C:GLU727
|
4.9
|
15.0
|
1.0
|
CG
|
C:GLU727
|
4.9
|
14.5
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 6zqz
Go back to
Magnesium Binding Sites List in 6zqz
Magnesium binding site 5 out
of 5 in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1002
b:11.8
occ:1.00
|
O
|
D:HOH1252
|
2.1
|
9.8
|
1.0
|
O
|
D:HOH1119
|
2.1
|
9.3
|
1.0
|
O
|
D:HOH1138
|
2.1
|
9.1
|
1.0
|
O
|
D:HOH1127
|
2.1
|
12.0
|
1.0
|
O
|
D:HOH1226
|
2.1
|
9.9
|
1.0
|
OD1
|
D:ASP697
|
2.2
|
9.7
|
1.0
|
CG
|
D:ASP697
|
3.1
|
10.3
|
1.0
|
OD2
|
D:ASP697
|
3.4
|
9.5
|
1.0
|
ZN
|
D:ZN1001
|
3.7
|
14.5
|
1.0
|
O
|
D:HOH1326
|
3.8
|
21.9
|
1.0
|
O
|
D:HOH1238
|
4.0
|
18.6
|
1.0
|
OE2
|
D:GLU727
|
4.1
|
11.9
|
1.0
|
CD2
|
D:HIS696
|
4.1
|
10.7
|
1.0
|
O
|
D:HOH1223
|
4.1
|
12.2
|
1.0
|
OG1
|
D:THR768
|
4.2
|
10.3
|
1.0
|
NE2
|
D:HIS730
|
4.2
|
10.2
|
1.0
|
O
|
D:HIS696
|
4.3
|
11.0
|
1.0
|
OD2
|
D:ASP808
|
4.4
|
13.5
|
1.0
|
CD2
|
D:HIS730
|
4.4
|
9.9
|
1.0
|
CD2
|
D:HIS700
|
4.4
|
14.4
|
1.0
|
NE2
|
D:HIS656
|
4.4
|
14.8
|
1.0
|
NE2
|
D:HIS696
|
4.5
|
11.2
|
1.0
|
CB
|
D:THR768
|
4.5
|
10.7
|
1.0
|
CD2
|
D:HIS656
|
4.5
|
14.9
|
1.0
|
CB
|
D:ASP697
|
4.5
|
10.7
|
1.0
|
NE2
|
D:HIS700
|
4.7
|
13.9
|
1.0
|
O
|
D:THR768
|
4.7
|
11.4
|
1.0
|
CA
|
D:ASP697
|
4.8
|
11.0
|
1.0
|
CG
|
D:GLU727
|
4.9
|
11.0
|
1.0
|
CD
|
D:GLU727
|
5.0
|
11.6
|
1.0
|
O
|
D:HOH1187
|
5.0
|
20.4
|
1.0
|
|
Reference:
G.Tresadern,
I.Velter,
A.A.Trabanco,
F.Van Den Keybus,
G.J.Macdonald,
M.V.F.Somers,
G.Vanhoof,
P.M.Leonard,
M.B.A.C.Lamers,
Y.E.M.Van Roosbroeck,
P.J.J.A.Buijnsters.
[1,2,4]Triazolo[1,5- A ]Pyrimidine Phosphodiesterase 2A Inhibitors: Structure and Free-Energy Perturbation-Guided Exploration. J.Med.Chem. V. 63 12887 2020.
ISSN: ISSN 0022-2623
PubMed: 33105987
DOI: 10.1021/ACS.JMEDCHEM.0C01272
Page generated: Wed Oct 2 02:36:15 2024
|