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Magnesium in PDB 5edh: Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7%

Enzymatic activity of Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7%

All present enzymatic activity of Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7%:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7%, PDB code: 5edh was solved by C.Joseph, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.68 / 2.03
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.401, 135.401, 235.335, 90.00, 90.00, 120.00
R / Rfree (%) 18.6 / 22.7

Other elements in 5edh:

The structure of Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7% also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7% (pdb code 5edh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7%, PDB code: 5edh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5edh

Go back to Magnesium Binding Sites List in 5edh
Magnesium binding site 1 out of 4 in the Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7%


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:27.6
occ:1.00
 O A:HOH999 2.0 23.9 1.0
OD1 A:ASP564 2.0 26.8 1.0
O A:HOH966 2.1 27.2 1.0
O A:HOH908 2.1 24.4 1.0
O A:HOH972 2.2 23.6 1.0
O A:HOH919 2.2 26.0 1.0
CG A:ASP564 3.0 29.1 1.0
OD2 A:ASP564 3.4 30.4 1.0
ZN A:ZN801 3.7 31.2 1.0
O A:HOH962 3.9 41.7 1.0
OE2 A:GLU592 4.1 28.6 1.0
NE2 A:HIS595 4.1 26.7 1.0
OG1 A:THR633 4.3 26.1 1.0
O A:HOH986 4.3 36.8 1.0
CD2 A:HIS563 4.3 26.6 1.0
CD2 A:HIS567 4.4 26.3 1.0
O A:HIS563 4.4 27.3 1.0
CB A:ASP564 4.4 27.3 1.0
CD2 A:HIS525 4.4 28.1 1.0
CD2 A:HIS595 4.5 24.1 1.0
NE2 A:HIS525 4.5 29.6 1.0
OD2 A:ASP674 4.5 30.9 1.0
O A:THR633 4.5 29.0 1.0
NE2 A:HIS567 4.6 25.3 1.0
NE2 A:HIS563 4.7 29.6 1.0
CB A:THR633 4.7 27.7 1.0
CA A:ASP564 4.8 27.9 1.0
CD A:GLU592 5.0 28.2 1.0
CG A:GLU592 5.0 25.4 1.0

Magnesium binding site 2 out of 4 in 5edh

Go back to Magnesium Binding Sites List in 5edh
Magnesium binding site 2 out of 4 in the Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7%


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:25.1
occ:1.00
 O B:HOH975 1.9 24.3 1.0
O B:HOH951 2.0 24.9 1.0
O B:HOH927 2.1 20.3 1.0
O B:HOH1004 2.1 23.1 1.0
OD1 B:ASP564 2.1 25.4 1.0
O B:HOH960 2.1 23.4 1.0
CG B:ASP564 3.1 25.1 1.0
OD2 B:ASP564 3.5 25.2 1.0
ZN B:ZN801 3.8 28.9 1.0
O B:HOH1042 3.8 47.2 1.0
OE2 B:GLU592 3.9 31.5 1.0
NE2 B:HIS595 4.0 22.9 1.0
O B:HOH956 4.2 27.6 1.0
O B:HOH915 4.2 50.9 1.0
CD2 B:HIS567 4.2 26.0 1.0
CD2 B:HIS563 4.3 25.1 1.0
OG1 B:THR633 4.3 24.2 1.0
CD2 B:HIS595 4.4 25.9 1.0
O B:HIS563 4.4 22.8 1.0
NE2 B:HIS567 4.4 26.3 1.0
OD2 B:ASP674 4.5 29.5 1.0
CD2 B:HIS525 4.5 24.1 1.0
CB B:ASP564 4.5 23.2 1.0
NE2 B:HIS525 4.6 26.8 1.0
O B:THR633 4.6 25.6 1.0
NE2 B:HIS563 4.7 25.5 1.0
CA B:ASP564 4.8 24.4 1.0
CB B:THR633 4.8 24.6 1.0
CD B:GLU592 4.8 28.7 1.0
CG B:GLU592 4.8 26.9 1.0

Magnesium binding site 3 out of 4 in 5edh

Go back to Magnesium Binding Sites List in 5edh
Magnesium binding site 3 out of 4 in the Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7%


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:26.1
occ:1.00
 O C:HOH954 2.0 24.6 1.0
O C:HOH943 2.0 25.1 1.0
O C:HOH983 2.1 25.7 1.0
OD1 C:ASP564 2.1 25.8 1.0
O C:HOH935 2.1 21.5 1.0
O C:HOH1001 2.1 23.4 1.0
CG C:ASP564 3.1 24.8 1.0
OD2 C:ASP564 3.5 24.8 1.0
ZN C:ZN801 3.8 31.0 1.0
O C:HOH1033 3.9 48.9 1.0
OE2 C:GLU592 4.0 30.6 1.0
O C:HOH941 4.0 49.2 1.0
NE2 C:HIS595 4.0 30.2 1.0
OG1 C:THR633 4.2 25.1 1.0
CD2 C:HIS567 4.2 27.4 1.0
O C:HIS563 4.2 26.2 1.0
CD2 C:HIS563 4.2 24.2 1.0
O C:HOH968 4.3 29.5 1.0
OD2 C:ASP674 4.4 31.7 1.0
CD2 C:HIS595 4.4 27.8 1.0
NE2 C:HIS567 4.4 27.9 1.0
CB C:ASP564 4.5 23.9 1.0
O C:THR633 4.5 25.5 1.0
CD2 C:HIS525 4.5 28.4 1.0
NE2 C:HIS525 4.6 29.4 1.0
CB C:THR633 4.6 25.1 1.0
NE2 C:HIS563 4.7 25.1 1.0
CG C:GLU592 4.8 26.6 1.0
CA C:ASP564 4.8 25.9 1.0
CD C:GLU592 4.8 27.5 1.0

Magnesium binding site 4 out of 4 in 5edh

Go back to Magnesium Binding Sites List in 5edh
Magnesium binding site 4 out of 4 in the Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7%


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:40.4
occ:1.00
 O D:HOH941 2.0 37.9 1.0
O D:HOH935 2.1 36.4 1.0
OD1 D:ASP564 2.1 34.0 1.0
O D:HOH923 2.2 30.2 1.0
O D:HOH905 2.2 34.8 1.0
O D:HOH903 2.3 34.1 1.0
CG D:ASP564 3.2 34.2 1.0
OD2 D:ASP564 3.5 36.0 1.0
ZN D:ZN801 3.8 39.8 1.0
O D:HOH914 3.8 53.8 1.0
O D:HOH939 3.9 45.4 1.0
NE2 D:HIS595 4.0 37.1 1.0
OE2 D:GLU592 4.0 37.8 1.0
CD2 D:HIS567 4.2 40.9 1.0
OG1 D:THR633 4.2 33.8 1.0
CD2 D:HIS595 4.3 34.6 1.0
O D:HIS563 4.4 31.1 1.0
NE2 D:HIS567 4.4 38.1 1.0
CD2 D:HIS525 4.4 37.3 1.0
CD2 D:HIS563 4.4 33.6 1.0
NE2 D:HIS525 4.5 43.1 1.0
CB D:ASP564 4.5 34.7 1.0
OD2 D:ASP674 4.6 35.8 1.0
O D:THR633 4.7 40.1 1.0
CA D:ASP564 4.8 33.4 1.0
CD D:GLU592 4.9 39.5 1.0
CB D:THR633 4.9 34.6 1.0
NE2 D:HIS563 4.9 33.8 1.0
CG D:GLU592 4.9 40.2 1.0

Reference:

B.Kuhn, W.Guba, J.Hert, D.Banner, C.Bissantz, S.Ceccarelli, W.Haap, M.Korner, A.Kuglstatter, C.Lerner, P.Mattei, W.Neidhart, E.Pinard, M.G.Rudolph, T.Schulz-Gasch, T.Woltering, M.Stahl. A Real-World Perspective on Molecular Design. J.Med.Chem. V. 59 4087 2016.
ISSN: ISSN 0022-2623
PubMed: 26878596
DOI: 10.1021/ACS.JMEDCHEM.5B01875
Page generated: Mon Dec 14 20:14:59 2020

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