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Magnesium in PDB 5sel: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3- Yl)Pyrazole-3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3- Yl)Pyrazole-3-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3- Yl)Pyrazole-3-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3- Yl)Pyrazole-3-Carboxamide, PDB code: 5sel was solved by C.Joseph, J.U.Peters, 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) 43.61 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.812, 134.812, 235.082, 90, 90, 120
R / Rfree (%) 18.4 / 23.1

Other elements in 5sel:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3- Yl)Pyrazole-3-Carboxamide 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 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3- Yl)Pyrazole-3-Carboxamide (pdb code 5sel). 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 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3- Yl)Pyrazole-3-Carboxamide, PDB code: 5sel:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sel

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3- Yl)Pyrazole-3-Carboxamide


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 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3- Yl)Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:25.8
occ:1.00
O A:HOH948 1.9 24.1 1.0
O A:HOH1005 1.9 22.2 1.0
O A:HOH944 2.0 23.6 1.0
OD1 A:ASP564 2.0 22.9 1.0
O A:HOH939 2.0 23.6 1.0
O A:HOH968 2.2 24.5 1.0
CG A:ASP564 3.0 27.3 1.0
OD2 A:ASP564 3.4 27.4 1.0
ZN A:ZN801 3.8 33.0 1.0
O A:HOH979 4.0 31.6 1.0
NE2 A:HIS595 4.0 27.6 1.0
OE2 A:GLU592 4.1 27.5 1.0
O A:HOH960 4.1 35.8 1.0
CD2 A:HIS567 4.3 32.2 1.0
CD2 A:HIS563 4.3 27.4 1.0
OG1 A:THR633 4.3 31.8 1.0
O A:HIS563 4.3 29.5 1.0
CD2 A:HIS595 4.3 28.1 1.0
CB A:ASP564 4.4 26.9 1.0
NE2 A:HIS567 4.5 34.3 1.0
O A:THR633 4.5 31.5 1.0
OD2 A:ASP674 4.5 35.4 1.0
CD2 A:HIS525 4.6 27.1 1.0
NE2 A:HIS525 4.6 26.5 1.0
CB A:THR633 4.7 29.9 1.0
NE2 A:HIS563 4.7 27.2 1.0
CA A:ASP564 4.7 28.4 1.0
CG A:GLU592 4.8 27.6 1.0
CD A:GLU592 4.9 29.7 1.0

Magnesium binding site 2 out of 4 in 5sel

Go back to Magnesium Binding Sites List in 5sel
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3- Yl)Pyrazole-3-Carboxamide


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 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3- Yl)Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:22.7
occ:1.00
O B:HOH926 1.9 25.9 1.0
O B:HOH948 2.0 21.7 1.0
O B:HOH904 2.0 18.4 1.0
O B:HOH988 2.0 22.1 1.0
O B:HOH945 2.1 19.0 1.0
OD1 B:ASP564 2.1 30.1 1.0
CG B:ASP564 3.1 28.0 1.0
OD2 B:ASP564 3.5 31.1 1.0
ZN B:ZN801 3.8 33.2 1.0
OE2 B:GLU592 4.0 33.8 1.0
NE2 B:HIS595 4.1 28.0 1.0
O B:HOH993 4.1 33.3 1.0
CD2 B:HIS563 4.2 29.1 1.0
O B:HOH980 4.3 31.2 1.0
OG1 B:THR633 4.3 26.8 1.0
OD2 B:ASP674 4.3 28.3 1.0
CD2 B:HIS595 4.4 28.7 1.0
CD2 B:HIS567 4.4 29.4 1.0
O B:HIS563 4.4 29.2 1.0
O B:THR633 4.4 26.7 1.0
NE2 B:HIS567 4.5 30.4 1.0
NE2 B:HIS563 4.5 29.0 1.0
CB B:ASP564 4.5 28.0 1.0
CD2 B:HIS525 4.6 29.8 1.0
NE2 B:HIS525 4.7 30.8 1.0
CB B:THR633 4.7 27.8 1.0
CG B:GLU592 4.7 31.6 1.0
CD B:GLU592 4.8 30.4 1.0
CA B:ASP564 4.8 29.4 1.0

Magnesium binding site 3 out of 4 in 5sel

Go back to Magnesium Binding Sites List in 5sel
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3- Yl)Pyrazole-3-Carboxamide


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 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3- Yl)Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:27.1
occ:1.00
O C:HOH943 1.9 20.8 1.0
O C:HOH942 2.0 26.9 1.0
O C:HOH940 2.0 25.8 1.0
OD1 C:ASP564 2.0 26.4 1.0
O C:HOH948 2.0 21.4 1.0
O C:HOH992 2.2 28.9 1.0
CG C:ASP564 3.1 26.8 1.0
OD2 C:ASP564 3.4 28.1 1.0
ZN C:ZN801 3.8 33.5 1.0
NE2 C:HIS595 4.0 31.8 1.0
O C:HOH962 4.0 34.3 1.0
OE2 C:GLU592 4.0 29.6 1.0
CD2 C:HIS567 4.1 28.7 1.0
O C:HOH971 4.2 33.2 1.0
OG1 C:THR633 4.2 26.0 1.0
CD2 C:HIS595 4.2 33.6 1.0
NE2 C:HIS567 4.3 30.5 1.0
O C:HIS563 4.4 29.1 1.0
CD2 C:HIS563 4.4 27.2 1.0
CB C:ASP564 4.4 25.2 1.0
OD2 C:ASP674 4.4 32.1 1.0
O C:THR633 4.5 32.8 1.0
CD2 C:HIS525 4.6 32.8 1.0
NE2 C:HIS525 4.6 33.4 1.0
CA C:ASP564 4.7 26.4 1.0
CB C:THR633 4.7 28.4 1.0
CG C:GLU592 4.8 28.9 1.0
CD C:GLU592 4.8 29.6 1.0
NE2 C:HIS563 4.8 29.5 1.0

Magnesium binding site 4 out of 4 in 5sel

Go back to Magnesium Binding Sites List in 5sel
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3- Yl)Pyrazole-3-Carboxamide


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 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3- Yl)Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:36.6
occ:1.00
O D:HOH967 1.9 30.5 1.0
O D:HOH957 1.9 29.6 1.0
O D:HOH954 2.0 33.6 1.0
O D:HOH913 2.1 30.5 1.0
OD1 D:ASP564 2.2 38.1 1.0
O D:HOH908 2.3 34.1 1.0
CG D:ASP564 3.1 36.5 1.0
OD2 D:ASP564 3.5 37.6 1.0
O D:HOH941 3.8 39.0 1.0
ZN D:ZN801 3.9 38.6 1.0
O D:HOH935 3.9 35.8 1.0
OE2 D:GLU592 4.0 35.9 1.0
NE2 D:HIS595 4.0 38.0 1.0
CD2 D:HIS567 4.1 36.9 1.0
NE2 D:HIS567 4.2 34.4 1.0
OG1 D:THR633 4.3 35.6 1.0
CD2 D:HIS595 4.3 38.8 1.0
O D:HIS563 4.3 33.1 1.0
CD2 D:HIS563 4.4 31.6 1.0
OD2 D:ASP674 4.5 40.9 1.0
CB D:ASP564 4.5 34.0 1.0
CD2 D:HIS525 4.6 40.2 1.0
NE2 D:HIS525 4.6 41.9 1.0
CB D:THR633 4.7 34.1 1.0
O D:THR633 4.7 37.4 1.0
CA D:ASP564 4.8 33.9 1.0
NE2 D:HIS563 4.8 30.4 1.0
CD D:GLU592 4.8 37.9 1.0
CG D:GLU592 4.9 39.2 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 19:20:28 2025

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