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Magnesium in PDB 5sfd: Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(2-Methyl-5-Piperidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(2-Methyl-5-Piperidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(2-Methyl-5-Piperidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(2-Methyl-5-Piperidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine, PDB code: 5sfd was solved by C.Joseph, A.Flohr, J.Benz, D.Schlatter, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.70 / 2.05
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.026, 135.026, 235.566, 90, 90, 120
R / Rfree (%) 18.2 / 23.1

Other elements in 5sfd:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(2-Methyl-5-Piperidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(2-Methyl-5-Piperidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine (pdb code 5sfd). 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 10 in Complex with 5,8- Dimethyl-2-[2-(2-Methyl-5-Piperidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine, PDB code: 5sfd:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sfd

Go back to Magnesium Binding Sites List in 5sfd
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(2-Methyl-5-Piperidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine


Mono view


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 10 in Complex with 5,8- Dimethyl-2-[2-(2-Methyl-5-Piperidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:27.0
occ:1.00
 O A:HOH987 2.0 22.4 1.0
OD1 A:ASP564 2.0 24.9 1.0
O A:HOH975 2.0 26.4 1.0
O A:HOH932 2.0 22.4 1.0
O A:HOH924 2.1 29.5 1.0
O A:HOH945 2.2 25.6 1.0
CG A:ASP564 3.1 30.0 1.0
OD2 A:ASP564 3.5 31.8 1.0
O A:HOH962 3.7 36.5 1.0
ZN A:ZN801 3.8 32.0 1.0
OE2 A:GLU592 3.9 36.3 1.0
O A:HOH967 4.1 31.3 1.0
NE2 A:HIS595 4.1 31.6 1.0
OG1 A:THR633 4.3 32.7 1.0
O A:HIS563 4.3 27.6 1.0
CD2 A:HIS563 4.4 28.1 1.0
CD2 A:HIS567 4.4 30.0 1.0
CD2 A:HIS595 4.4 29.4 1.0
CB A:ASP564 4.4 25.4 1.0
O A:THR633 4.4 28.0 1.0
CD2 A:HIS525 4.5 27.9 1.0
NE2 A:HIS525 4.5 30.2 1.0
OD2 A:ASP674 4.6 30.4 1.0
NE2 A:HIS567 4.6 27.7 1.0
CB A:THR633 4.7 27.8 1.0
CA A:ASP564 4.8 28.7 1.0
CD A:GLU592 4.8 32.0 1.0
CG A:GLU592 4.8 27.7 1.0
NE2 A:HIS563 4.9 28.1 1.0

Magnesium binding site 2 out of 4 in 5sfd

Go back to Magnesium Binding Sites List in 5sfd
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(2-Methyl-5-Piperidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine


Mono view


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 10 in Complex with 5,8- Dimethyl-2-[2-(2-Methyl-5-Piperidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:25.5
occ:1.00
 O B:HOH965 1.9 19.4 1.0
O B:HOH997 2.0 23.7 1.0
O B:HOH951 2.0 23.8 1.0
O B:HOH920 2.1 22.4 1.0
OD1 B:ASP564 2.1 24.1 1.0
O B:HOH946 2.2 23.3 1.0
CG B:ASP564 3.2 24.5 1.0
OD2 B:ASP564 3.5 25.0 1.0
O B:HOH939 3.6 40.9 1.0
ZN B:ZN801 3.8 30.6 1.0
O B:HOH1027 3.9 49.4 1.0
OE2 B:GLU592 4.0 33.9 1.0
NE2 B:HIS595 4.1 23.3 1.0
O B:HOH942 4.2 27.3 1.0
CD2 B:HIS567 4.3 27.6 1.0
CD2 B:HIS563 4.3 26.5 1.0
NE2 B:HIS567 4.3 27.8 1.0
OG1 B:THR633 4.3 25.0 1.0
O B:HIS563 4.3 28.0 1.0
OD2 B:ASP674 4.3 33.0 1.0
CD2 B:HIS595 4.4 27.4 1.0
CD2 B:HIS525 4.4 29.3 1.0
CB B:ASP564 4.5 24.0 1.0
O B:THR633 4.5 24.5 1.0
NE2 B:HIS525 4.6 38.4 1.0
NE2 B:HIS563 4.6 26.4 1.0
CB B:THR633 4.7 25.6 1.0
CA B:ASP564 4.7 25.9 1.0
CG B:GLU592 4.8 30.7 1.0
CD B:GLU592 4.8 31.1 1.0

Magnesium binding site 3 out of 4 in 5sfd

Go back to Magnesium Binding Sites List in 5sfd
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(2-Methyl-5-Piperidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine


Mono view


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 10 in Complex with 5,8- Dimethyl-2-[2-(2-Methyl-5-Piperidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:28.4
occ:1.00
 OD1 C:ASP564 2.0 28.3 1.0
O C:HOH965 2.1 23.8 1.0
O C:HOH944 2.1 25.3 1.0
O C:HOH912 2.1 28.2 1.0
O C:HOH927 2.1 24.4 1.0
O C:HOH985 2.2 25.0 1.0
CG C:ASP564 3.1 27.7 1.0
OD2 C:ASP564 3.5 28.8 1.0
ZN C:ZN801 3.8 31.4 1.0
OE2 C:GLU592 3.9 28.1 1.0
NE2 C:HIS595 3.9 31.3 1.0
O C:HOH1006 4.0 45.8 1.0
OG1 C:THR633 4.1 23.3 1.0
O C:HOH913 4.1 45.5 1.0
CD2 C:HIS567 4.1 27.0 1.0
O C:HIS563 4.1 24.6 1.0
CD2 C:HIS595 4.2 28.3 1.0
CD2 C:HIS563 4.3 23.9 1.0
NE2 C:HIS567 4.3 28.7 1.0
O C:HOH950 4.3 31.1 1.0
CB C:ASP564 4.4 23.8 1.0
O C:THR633 4.5 31.7 1.0
OD2 C:ASP674 4.5 28.9 1.0
CB C:THR633 4.6 27.1 1.0
CD2 C:HIS525 4.6 36.8 1.0
NE2 C:HIS525 4.7 33.1 1.0
CA C:ASP564 4.7 27.1 1.0
CG C:GLU592 4.7 29.1 1.0
CD C:GLU592 4.7 32.2 1.0
NE2 C:HIS563 4.8 23.2 1.0
C C:HIS563 5.0 28.7 1.0

Magnesium binding site 4 out of 4 in 5sfd

Go back to Magnesium Binding Sites List in 5sfd
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(2-Methyl-5-Piperidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine


Mono view


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 10 in Complex with 5,8- Dimethyl-2-[2-(2-Methyl-5-Piperidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:35.9
occ:1.00
 O D:HOH947 2.0 36.7 1.0
O D:HOH944 2.0 24.8 1.0
O D:HOH924 2.1 27.1 1.0
OD1 D:ASP564 2.1 30.9 1.0
O D:HOH902 2.2 33.6 1.0
O D:HOH908 2.2 37.7 1.0
CG D:ASP564 3.1 32.6 1.0
OD2 D:ASP564 3.5 40.3 1.0
ZN D:ZN801 3.8 39.6 1.0
O D:HOH921 3.8 40.3 1.0
OE2 D:GLU592 3.9 35.8 1.0
O D:HOH915 4.0 43.7 1.0
NE2 D:HIS595 4.0 36.0 1.0
CD2 D:HIS567 4.2 42.2 1.0
OG1 D:THR633 4.3 38.2 1.0
NE2 D:HIS567 4.4 36.2 1.0
O D:HIS563 4.4 32.3 1.0
CD2 D:HIS595 4.4 38.9 1.0
CD2 D:HIS563 4.4 33.3 1.0
CD2 D:HIS525 4.4 39.1 1.0
OD2 D:ASP674 4.5 33.4 1.0
CB D:ASP564 4.5 32.5 1.0
O D:THR633 4.5 43.3 1.0
NE2 D:HIS525 4.5 46.1 1.0
CB D:THR633 4.8 38.4 1.0
NE2 D:HIS563 4.8 34.4 1.0
CA D:ASP564 4.8 29.8 1.0
CD D:GLU592 4.8 38.0 1.0
O D:HOH953 4.9 36.8 1.0
CG D:GLU592 5.0 40.0 1.0
CE1 D:HIS595 5.0 36.7 1.0

Reference:

A.Tosstorff, M.G.Rudolph, J.C.Cole, M.Reutlinger, C.Kramer, H.Schaffhauser, A.Nilly, A.Flohr, B.Kuhn. A High Quality, Industrial Data Set For Binding Affinity Prediction: Performance Comparison in Different Early Drug Discovery Scenarios. J.Comput.Aided Mol.Des. V. 36 753 2022.
ISSN: ESSN 1573-4951
PubMed: 36153472
DOI: 10.1007/S10822-022-00478-X
Page generated: Tue Aug 12 19:27:55 2025

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