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Magnesium in PDB 5ede: Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A

Enzymatic activity of Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A

All present enzymatic activity of Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A, PDB code: 5ede 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) 43.73 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.610, 135.610, 235.660, 90.00, 90.00, 120.00
R / Rfree (%) 18.4 / 24.2

Other elements in 5ede:

The structure of Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A 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 in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A (pdb code 5ede). 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 in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A, PDB code: 5ede:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5ede

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Magnesium binding site 1 out of 4 in the Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:25.4
occ:1.00
 OD1 A:ASP564 2.0 21.9 1.0
O A:HOH1048 2.1 21.9 1.0
O A:HOH931 2.1 13.6 1.0
O A:HOH975 2.2 24.0 1.0
O A:HOH978 2.2 26.2 1.0
O A:HOH970 2.2 30.3 1.0
CG A:ASP564 3.0 22.8 1.0
OD2 A:ASP564 3.3 24.1 1.0
O A:HOH1016 3.8 27.2 1.0
ZN A:ZN801 3.8 28.4 1.0
NE2 A:HIS595 4.1 19.0 1.0
O A:HOH990 4.2 29.9 1.0
OE2 A:GLU592 4.2 19.6 1.0
O A:HIS563 4.3 24.9 1.0
O A:HOH1084 4.3 39.2 1.0
CD2 A:HIS567 4.3 28.6 1.0
CD2 A:HIS563 4.3 16.9 1.0
OG1 A:THR633 4.4 25.1 1.0
CB A:ASP564 4.4 20.4 1.0
CD2 A:HIS595 4.5 18.5 1.0
O A:THR633 4.5 23.3 1.0
CD2 A:HIS525 4.6 24.0 1.0
NE2 A:HIS563 4.6 18.9 1.0
NE2 A:HIS567 4.6 28.5 1.0
NE2 A:HIS525 4.6 21.3 1.0
CB A:THR633 4.7 24.4 1.0
OD2 A:ASP674 4.8 31.5 1.0
CA A:ASP564 4.8 21.8 1.0
CG A:GLU592 4.9 24.5 1.0
CD A:GLU592 5.0 24.3 1.0

Magnesium binding site 2 out of 4 in 5ede

Go back to Magnesium Binding Sites List in 5ede
Magnesium binding site 2 out of 4 in the Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:12.3
occ:1.00
 O B:HOH977 1.9 13.9 1.0
O B:HOH924 2.0 14.6 1.0
O B:HOH1040 2.1 14.2 1.0
O B:HOH972 2.1 17.0 1.0
O B:HOH919 2.1 12.2 1.0
OD1 B:ASP564 2.1 25.2 1.0
CG B:ASP564 3.2 22.7 1.0
OD2 B:ASP564 3.5 16.4 1.0
O B:HOH1010 3.7 29.7 1.0
ZN B:ZN801 3.7 24.2 1.0
O B:HOH1054 3.9 41.7 1.0
NE2 B:HIS595 4.0 21.4 1.0
OE2 B:GLU592 4.1 24.4 1.0
OG1 B:THR633 4.2 21.2 1.0
O B:HIS563 4.2 25.0 1.0
CD2 B:HIS563 4.2 13.2 1.0
CD2 B:HIS595 4.3 23.0 1.0
O B:HOH998 4.4 22.7 1.0
CD2 B:HIS567 4.4 21.6 1.0
O B:THR633 4.5 22.3 1.0
OD2 B:ASP674 4.5 16.0 1.0
NE2 B:HIS567 4.5 18.2 1.0
CB B:ASP564 4.6 17.2 1.0
NE2 B:HIS563 4.6 17.5 1.0
CB B:THR633 4.6 22.6 1.0
CD2 B:HIS525 4.7 23.9 1.0
NE2 B:HIS525 4.7 28.4 1.0
CG B:GLU592 4.8 24.3 1.0
CA B:ASP564 4.8 19.1 1.0
CD B:GLU592 4.9 25.4 1.0

Magnesium binding site 3 out of 4 in 5ede

Go back to Magnesium Binding Sites List in 5ede
Magnesium binding site 3 out of 4 in the Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:22.6
occ:1.00
 O C:HOH956 2.0 18.9 1.0
O C:HOH1036 2.1 23.4 1.0
OD1 C:ASP564 2.1 26.0 1.0
O C:HOH946 2.1 27.1 1.0
O C:HOH935 2.1 24.4 1.0
O C:HOH950 2.1 19.6 1.0
CG C:ASP564 3.1 19.9 1.0
OD2 C:ASP564 3.4 17.8 1.0
O C:HOH963 3.9 37.2 1.0
ZN C:ZN801 3.9 26.1 1.0
OE2 C:GLU592 3.9 29.1 1.0
NE2 C:HIS595 4.0 26.6 1.0
O C:HOH1083 4.1 50.6 1.0
CD2 C:HIS567 4.2 22.6 1.0
O C:HIS563 4.2 19.6 1.0
OG1 C:THR633 4.3 21.6 1.0
O C:HOH1033 4.3 25.1 1.0
CD2 C:HIS563 4.3 19.4 1.0
CD2 C:HIS595 4.3 23.4 1.0
CB C:ASP564 4.4 17.4 1.0
NE2 C:HIS567 4.5 24.1 1.0
O C:THR633 4.5 27.2 1.0
OD2 C:ASP674 4.5 25.7 1.0
CB C:THR633 4.6 23.7 1.0
NE2 C:HIS525 4.7 26.6 1.0
CD2 C:HIS525 4.7 26.3 1.0
CA C:ASP564 4.8 19.1 1.0
CD C:GLU592 4.8 26.3 1.0
NE2 C:HIS563 4.8 24.5 1.0
CG C:GLU592 4.8 27.4 1.0

Magnesium binding site 4 out of 4 in 5ede

Go back to Magnesium Binding Sites List in 5ede
Magnesium binding site 4 out of 4 in the Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human PDE10A in Complex with 1-(4-Chloro-Phenyl)-3-Methyl-1H-Thieno[2, 3-C]Pyrazole-5-Carboxylic Acid (Tetrahydro-Furan-2-Ylmethyl)-Amide at 2.2A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:31.0
occ:1.00
 O D:HOH988 1.9 24.4 1.0
O D:HOH934 1.9 26.1 1.0
OD1 D:ASP564 2.1 28.3 1.0
O D:HOH993 2.1 23.3 1.0
O D:HOH939 2.3 17.9 1.0
O D:HOH905 2.3 27.6 1.0
CG D:ASP564 3.1 30.4 1.0
OD2 D:ASP564 3.5 27.3 1.0
O D:HOH955 3.9 47.0 1.0
NE2 D:HIS595 3.9 27.3 1.0
ZN D:ZN801 3.9 33.4 1.0
O D:HOH991 4.1 34.2 1.0
OE2 D:GLU592 4.1 25.8 1.0
CD2 D:HIS595 4.2 28.6 1.0
OG1 D:THR633 4.2 30.7 1.0
O D:HIS563 4.3 27.9 1.0
CD2 D:HIS567 4.3 32.5 1.0
O D:THR633 4.3 33.2 1.0
CD2 D:HIS563 4.4 22.4 1.0
CB D:ASP564 4.5 27.8 1.0
NE2 D:HIS567 4.5 30.5 1.0
CD2 D:HIS525 4.6 32.2 1.0
OD2 D:ASP674 4.6 32.9 1.0
NE2 D:HIS525 4.6 34.7 1.0
CB D:THR633 4.8 30.4 1.0
CA D:ASP564 4.8 28.1 1.0
CG D:GLU592 4.8 31.4 1.0
NE2 D:HIS563 4.8 22.1 1.0
CD D:GLU592 4.9 31.9 1.0
CE1 D:HIS595 5.0 29.8 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 03:37:40 2024

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