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Magnesium in PDB 5edi: Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5%

Enzymatic activity of Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5%

All present enzymatic activity of Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5%:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5%, PDB code: 5edi 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) 43.60 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.231, 135.231, 235.395, 90.00, 90.00, 120.00
R / Rfree (%) 18.6 / 23.5

Other elements in 5edi:

The structure of Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5% also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5% (pdb code 5edi). 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, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5%, PDB code: 5edi:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5edi

Go back to Magnesium Binding Sites List in 5edi
Magnesium binding site 1 out of 4 in the Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5%


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:35.6
occ:1.00
 O A:HOH953 1.9 34.9 1.0
OD1 A:ASP564 2.0 35.7 1.0
O A:HOH973 2.1 31.9 1.0
O A:HOH911 2.1 27.4 1.0
O A:HOH940 2.2 36.0 1.0
O A:HOH928 2.2 32.4 1.0
CG A:ASP564 3.1 37.0 1.0
OD2 A:ASP564 3.4 39.1 1.0
ZN A:ZN801 3.7 40.5 1.0
O A:HOH960 3.8 46.5 1.0
NE2 A:HIS595 4.0 32.0 1.0
OE2 A:GLU592 4.1 38.5 1.0
O A:HOH970 4.3 40.0 1.0
CD2 A:HIS563 4.3 34.1 1.0
CD2 A:HIS567 4.4 35.1 1.0
OG1 A:THR633 4.4 37.0 1.0
CD2 A:HIS595 4.4 32.5 1.0
O A:HIS563 4.4 36.3 1.0
CD2 A:HIS525 4.4 39.9 1.0
CB A:ASP564 4.4 32.2 1.0
NE2 A:HIS525 4.5 37.1 1.0
OD2 A:ASP674 4.5 36.9 1.0
O A:THR633 4.6 36.8 1.0
NE2 A:HIS563 4.7 33.1 1.0
NE2 A:HIS567 4.7 36.6 1.0
CA A:ASP564 4.8 33.1 1.0
CB A:THR633 4.8 36.5 1.0
CG A:GLU592 4.9 36.0 1.0
CD A:GLU592 4.9 38.9 1.0

Magnesium binding site 2 out of 4 in 5edi

Go back to Magnesium Binding Sites List in 5edi
Magnesium binding site 2 out of 4 in the Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5%


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5% within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:29.6
occ:1.00
 O B:HOH922 2.0 34.3 1.0
O B:HOH979 2.0 31.0 1.0
O B:HOH960 2.0 24.8 1.0
O B:HOH937 2.1 29.8 1.0
O B:HOH902 2.1 29.3 1.0
OD1 B:ASP564 2.1 30.6 1.0
CG B:ASP564 3.2 30.9 1.0
OD2 B:ASP564 3.5 33.3 1.0
ZN B:ZN801 3.8 39.6 1.0
OE2 B:GLU592 3.9 38.1 1.0
O B:HOH977 3.9 47.2 1.0
O B:HOH952 4.1 37.8 1.0
NE2 B:HIS595 4.1 37.6 1.0
OG1 B:THR633 4.2 31.2 1.0
CD2 B:HIS563 4.2 34.8 1.0
CD2 B:HIS567 4.3 35.9 1.0
CD2 B:HIS595 4.4 38.9 1.0
OD2 B:ASP674 4.4 33.3 1.0
O B:HIS563 4.5 37.9 1.0
NE2 B:HIS567 4.5 36.4 1.0
NE2 B:HIS563 4.5 32.8 1.0
O B:THR633 4.5 37.6 1.0
CD2 B:HIS525 4.5 41.4 1.0
CB B:ASP564 4.5 31.2 1.0
NE2 B:HIS525 4.6 43.5 1.0
CB B:THR633 4.7 32.3 1.0
CD B:GLU592 4.8 35.8 1.0
CG B:GLU592 4.8 32.2 1.0
CA B:ASP564 4.9 35.0 1.0

Magnesium binding site 3 out of 4 in 5edi

Go back to Magnesium Binding Sites List in 5edi
Magnesium binding site 3 out of 4 in the Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5%


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5% within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:32.9
occ:1.00
 O C:HOH937 2.0 37.2 1.0
O C:HOH956 2.0 30.7 1.0
O C:HOH933 2.0 31.5 1.0
OD1 C:ASP564 2.1 35.7 1.0
O C:HOH925 2.1 28.9 1.0
O C:HOH975 2.2 34.4 1.0
CG C:ASP564 3.1 36.9 1.0
OD2 C:ASP564 3.5 38.6 1.0
ZN C:ZN801 3.8 40.7 1.0
O C:HOH1005 3.8 52.0 1.0
OE2 C:GLU592 4.0 41.4 1.0
O C:HOH938 4.0 52.0 1.0
NE2 C:HIS595 4.0 40.5 1.0
OG1 C:THR633 4.1 37.5 1.0
CD2 C:HIS563 4.2 30.1 1.0
O C:HOH962 4.2 39.8 1.0
O C:HIS563 4.3 32.4 1.0
CD2 C:HIS567 4.3 34.9 1.0
CD2 C:HIS595 4.4 38.7 1.0
OD2 C:ASP674 4.4 41.5 1.0
O C:THR633 4.4 41.4 1.0
CB C:ASP564 4.5 32.8 1.0
CB C:THR633 4.6 38.0 1.0
NE2 C:HIS567 4.6 37.9 1.0
NE2 C:HIS563 4.6 32.5 1.0
CD2 C:HIS525 4.6 38.1 1.0
NE2 C:HIS525 4.7 38.3 1.0
CG C:GLU592 4.7 34.1 1.0
CA C:ASP564 4.8 34.0 1.0
CD C:GLU592 4.8 36.5 1.0
O C:HOH995 5.0 42.0 1.0

Magnesium binding site 4 out of 4 in 5edi

Go back to Magnesium Binding Sites List in 5edi
Magnesium binding site 4 out of 4 in the Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5%


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5% within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:54.8
occ:1.00
 O D:HOH927 2.1 39.3 1.0
OD1 D:ASP564 2.1 51.6 1.0
O D:HOH920 2.1 45.9 1.0
O D:HOH901 2.1 49.5 1.0
O D:HOH925 2.2 55.0 1.0
O D:HOH906 2.2 51.0 1.0
CG D:ASP564 3.1 50.6 1.0
OD2 D:ASP564 3.4 60.5 1.0
O D:HOH915 3.7 49.0 1.0
ZN D:ZN801 3.8 57.9 1.0
NE2 D:HIS595 3.8 61.8 1.0
OE2 D:GLU592 3.9 52.9 1.0
O D:HOH928 4.0 52.2 1.0
CD2 D:HIS567 4.1 54.1 1.0
CD2 D:HIS595 4.2 59.4 1.0
OG1 D:THR633 4.3 51.9 1.0
CD2 D:HIS563 4.3 46.2 1.0
O D:HIS563 4.4 53.8 1.0
NE2 D:HIS567 4.4 54.0 1.0
CB D:ASP564 4.4 49.5 1.0
CD2 D:HIS525 4.4 56.6 1.0
NE2 D:HIS525 4.5 59.1 1.0
OD2 D:ASP674 4.6 56.5 1.0
O D:THR633 4.7 49.8 1.0
CA D:ASP564 4.7 51.8 1.0
NE2 D:HIS563 4.7 46.9 1.0
CB D:THR633 4.8 54.2 1.0
CE1 D:HIS595 4.9 57.4 1.0
CD D:GLU592 4.9 55.4 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: Sun Sep 29 03:37:54 2024

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