Magnesium in PDB 5tza: Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine
Enzymatic activity of Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine
All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine:
3.1.4.17;
Protein crystallography data
The structure of Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine, PDB code: 5tza
was solved by
R.Xu,
K.Aertgeerts,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
55.77 /
1.70
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
55.799,
73.444,
91.614,
109.36,
91.17,
91.14
|
R / Rfree (%)
|
16.5 /
19.7
|
Other elements in 5tza:
The structure of Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine
(pdb code 5tza). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine, PDB code: 5tza:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 5tza
Go back to
Magnesium Binding Sites List in 5tza
Magnesium binding site 1 out
of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine
![](/pictures/MG/pdb/tz/5tza-MG-sphere_01.jpg) Mono view
![](/pictures/MG/pdb/tz/5tza-MG-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1003
b:8.7
occ:1.00
|
O
|
A:HOH1174
|
2.0
|
10.0
|
1.0
|
O
|
A:HOH1201
|
2.1
|
10.6
|
1.0
|
O
|
A:HOH1234
|
2.1
|
10.2
|
1.0
|
O
|
A:HOH1154
|
2.1
|
8.3
|
1.0
|
OD1
|
A:ASP697
|
2.1
|
7.8
|
1.0
|
O
|
A:HOH1226
|
2.2
|
9.6
|
1.0
|
CG
|
A:ASP697
|
3.1
|
7.7
|
1.0
|
OD2
|
A:ASP697
|
3.4
|
9.2
|
1.0
|
ZN
|
A:ZN1002
|
3.7
|
11.8
|
1.0
|
O
|
A:HOH1370
|
3.9
|
15.9
|
1.0
|
O
|
A:HOH1277
|
3.9
|
14.8
|
1.0
|
OE2
|
A:GLU727
|
4.1
|
14.8
|
1.0
|
CD2
|
A:HIS696
|
4.1
|
11.1
|
1.0
|
NE2
|
A:HIS730
|
4.1
|
8.4
|
1.0
|
OG1
|
A:THR768
|
4.2
|
8.9
|
1.0
|
O
|
A:HOH1257
|
4.3
|
11.6
|
1.0
|
O
|
A:HIS696
|
4.4
|
8.4
|
1.0
|
CD2
|
A:HIS730
|
4.4
|
9.6
|
1.0
|
OD2
|
A:ASP808
|
4.4
|
13.6
|
1.0
|
CD2
|
A:HIS656
|
4.5
|
11.1
|
1.0
|
CB
|
A:ASP697
|
4.5
|
10.2
|
1.0
|
NE2
|
A:HIS656
|
4.5
|
12.9
|
1.0
|
CB
|
A:THR768
|
4.5
|
8.0
|
1.0
|
NE2
|
A:HIS696
|
4.5
|
7.6
|
1.0
|
CD2
|
A:HIS700
|
4.6
|
9.6
|
1.0
|
O
|
A:THR768
|
4.7
|
11.7
|
1.0
|
CA
|
A:ASP697
|
4.8
|
7.6
|
1.0
|
NE2
|
A:HIS700
|
4.9
|
10.6
|
1.0
|
CG
|
A:GLU727
|
4.9
|
10.2
|
1.0
|
CD
|
A:GLU727
|
4.9
|
13.4
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 5tza
Go back to
Magnesium Binding Sites List in 5tza
Magnesium binding site 2 out
of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine
![](/pictures/MG/pdb/tz/5tza-MG-sphere_02.jpg) Mono view
![](/pictures/MG/pdb/tz/5tza-MG-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1003
b:10.2
occ:1.00
|
O
|
B:HOH1130
|
2.0
|
10.8
|
1.0
|
O
|
B:HOH1156
|
2.1
|
9.8
|
1.0
|
OD1
|
B:ASP697
|
2.1
|
9.7
|
1.0
|
O
|
B:HOH1249
|
2.1
|
10.7
|
1.0
|
O
|
B:HOH1229
|
2.1
|
11.8
|
1.0
|
O
|
B:HOH1208
|
2.2
|
11.4
|
1.0
|
CG
|
B:ASP697
|
3.1
|
10.0
|
1.0
|
OD2
|
B:ASP697
|
3.4
|
10.3
|
1.0
|
ZN
|
B:ZN1002
|
3.7
|
12.7
|
1.0
|
O
|
B:HOH1235
|
3.9
|
17.6
|
1.0
|
O
|
B:HOH1341
|
4.0
|
19.9
|
1.0
|
CD2
|
B:HIS696
|
4.1
|
9.5
|
1.0
|
OG1
|
B:THR768
|
4.1
|
10.3
|
1.0
|
OE2
|
B:GLU727
|
4.1
|
14.2
|
1.0
|
NE2
|
B:HIS730
|
4.2
|
10.1
|
1.0
|
O
|
B:HIS696
|
4.3
|
9.9
|
1.0
|
O
|
B:HOH1261
|
4.3
|
14.4
|
1.0
|
OD2
|
B:ASP808
|
4.3
|
13.3
|
1.0
|
CD2
|
B:HIS730
|
4.4
|
11.3
|
1.0
|
CB
|
B:ASP697
|
4.5
|
10.9
|
1.0
|
NE2
|
B:HIS696
|
4.5
|
9.4
|
1.0
|
CB
|
B:THR768
|
4.5
|
11.9
|
1.0
|
CD2
|
B:HIS656
|
4.5
|
14.5
|
1.0
|
NE2
|
B:HIS656
|
4.5
|
14.7
|
1.0
|
CD2
|
B:HIS700
|
4.6
|
14.6
|
1.0
|
O
|
B:THR768
|
4.7
|
11.6
|
1.0
|
CA
|
B:ASP697
|
4.8
|
10.3
|
1.0
|
O
|
B:HOH1118
|
4.9
|
26.4
|
1.0
|
NE2
|
B:HIS700
|
4.9
|
13.5
|
1.0
|
CG
|
B:GLU727
|
5.0
|
10.4
|
1.0
|
CD
|
B:GLU727
|
5.0
|
11.5
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 5tza
Go back to
Magnesium Binding Sites List in 5tza
Magnesium binding site 3 out
of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine
![](/pictures/MG/pdb/tz/5tza-MG-sphere_03.jpg) Mono view
![](/pictures/MG/pdb/tz/5tza-MG-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1003
b:11.1
occ:1.00
|
O
|
C:HOH1167
|
2.1
|
11.5
|
1.0
|
O
|
C:HOH1229
|
2.1
|
11.0
|
1.0
|
OD1
|
C:ASP697
|
2.1
|
10.1
|
1.0
|
O
|
C:HOH1132
|
2.1
|
12.3
|
1.0
|
O
|
C:HOH1121
|
2.1
|
11.5
|
1.0
|
O
|
C:HOH1215
|
2.1
|
10.6
|
1.0
|
CG
|
C:ASP697
|
3.1
|
13.1
|
1.0
|
OD2
|
C:ASP697
|
3.4
|
11.2
|
1.0
|
ZN
|
C:ZN1002
|
3.7
|
13.3
|
1.0
|
O
|
C:HOH1319
|
3.8
|
19.9
|
1.0
|
OE2
|
C:GLU727
|
4.0
|
13.2
|
1.0
|
O
|
C:HOH1231
|
4.1
|
19.2
|
1.0
|
OG1
|
C:THR768
|
4.2
|
9.8
|
1.0
|
NE2
|
C:HIS730
|
4.2
|
10.0
|
1.0
|
CD2
|
C:HIS696
|
4.2
|
13.1
|
1.0
|
O
|
C:HOH1251
|
4.2
|
12.4
|
1.0
|
O
|
C:HIS696
|
4.3
|
9.8
|
1.0
|
CD2
|
C:HIS656
|
4.4
|
14.2
|
1.0
|
CD2
|
C:HIS700
|
4.4
|
10.9
|
1.0
|
CB
|
C:ASP697
|
4.4
|
12.9
|
1.0
|
OD2
|
C:ASP808
|
4.4
|
15.5
|
1.0
|
CD2
|
C:HIS730
|
4.5
|
9.1
|
1.0
|
NE2
|
C:HIS656
|
4.5
|
18.0
|
1.0
|
CB
|
C:THR768
|
4.6
|
10.7
|
1.0
|
O
|
C:THR768
|
4.6
|
12.9
|
1.0
|
NE2
|
C:HIS696
|
4.7
|
10.2
|
1.0
|
NE2
|
C:HIS700
|
4.7
|
11.1
|
1.0
|
CA
|
C:ASP697
|
4.8
|
11.7
|
1.0
|
CD
|
C:GLU727
|
4.9
|
13.9
|
1.0
|
CG
|
C:GLU727
|
5.0
|
9.5
|
1.0
|
O
|
C:HOH1136
|
5.0
|
24.1
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 5tza
Go back to
Magnesium Binding Sites List in 5tza
Magnesium binding site 4 out
of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine
![](/pictures/MG/pdb/tz/5tza-MG-sphere_04.jpg) Mono view
![](/pictures/MG/pdb/tz/5tza-MG-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1003
b:9.5
occ:1.00
|
O
|
D:HOH1167
|
2.0
|
11.7
|
1.0
|
O
|
D:HOH1278
|
2.1
|
10.7
|
1.0
|
OD1
|
D:ASP697
|
2.1
|
9.1
|
1.0
|
O
|
D:HOH1143
|
2.1
|
9.3
|
1.0
|
O
|
D:HOH1169
|
2.2
|
11.0
|
1.0
|
O
|
D:HOH1237
|
2.2
|
10.2
|
1.0
|
CG
|
D:ASP697
|
3.0
|
9.4
|
1.0
|
OD2
|
D:ASP697
|
3.3
|
10.1
|
1.0
|
ZN
|
D:ZN1002
|
3.7
|
13.0
|
1.0
|
O
|
D:HOH1350
|
3.9
|
18.8
|
1.0
|
O
|
D:HOH1252
|
4.0
|
16.0
|
1.0
|
OE2
|
D:GLU727
|
4.1
|
12.3
|
1.0
|
CD2
|
D:HIS696
|
4.1
|
11.6
|
1.0
|
NE2
|
D:HIS730
|
4.2
|
8.8
|
1.0
|
O
|
D:HOH1241
|
4.2
|
12.9
|
1.0
|
OG1
|
D:THR768
|
4.2
|
10.1
|
1.0
|
O
|
D:HIS696
|
4.3
|
8.8
|
1.0
|
CD2
|
D:HIS700
|
4.4
|
13.2
|
1.0
|
CB
|
D:ASP697
|
4.4
|
11.5
|
1.0
|
OD2
|
D:ASP808
|
4.4
|
14.3
|
1.0
|
CD2
|
D:HIS656
|
4.5
|
12.3
|
1.0
|
CD2
|
D:HIS730
|
4.5
|
8.8
|
1.0
|
NE2
|
D:HIS656
|
4.5
|
13.3
|
1.0
|
NE2
|
D:HIS696
|
4.5
|
10.0
|
1.0
|
CB
|
D:THR768
|
4.5
|
9.8
|
1.0
|
NE2
|
D:HIS700
|
4.7
|
11.0
|
1.0
|
CA
|
D:ASP697
|
4.8
|
9.2
|
1.0
|
O
|
D:THR768
|
4.8
|
11.4
|
1.0
|
O
|
D:HOH1140
|
4.8
|
20.8
|
1.0
|
CD
|
D:GLU727
|
5.0
|
12.3
|
1.0
|
|
Reference:
L.Gomez,
M.E.Massari,
T.Vickers,
G.Freestone,
W.Vernier,
K.Ly,
R.Xu,
M.Mccarrick,
T.Marrone,
M.Metz,
Y.G.Yan,
Z.W.Yoder,
R.Lemus,
N.J.Broadbent,
R.Barido,
N.Warren,
K.Schmelzer,
D.Neul,
D.Lee,
C.B.Andersen,
K.Sebring,
K.Aertgeerts,
X.Zhou,
A.Tabatabaei,
M.Peters,
J.G.Breitenbucher.
Design and Synthesis of Novel and Selective Phosphodiesterase 2 (PDE2A) Inhibitors For the Treatment of Memory Disorders. J. Med. Chem. V. 60 2037 2017.
ISSN: ISSN 1520-4804
PubMed: 28165743
DOI: 10.1021/ACS.JMEDCHEM.6B01793
Page generated: Mon Dec 14 21:13:34 2020
|