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Magnesium in PDB 5sfr: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide, PDB code: 5sfr was solved by C.Joseph, L.Gobbi, 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) 43.77 / 2.04
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.625, 135.625, 235.847, 90, 90, 120
R / Rfree (%) 18.1 / 21.3

Other elements in 5sfr:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Fluorine (F) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide (pdb code 5sfr). 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-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide, PDB code: 5sfr:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sfr

Go back to Magnesium Binding Sites List in 5sfr
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide


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-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:24.5
occ:1.00
 O A:HOH1022 1.9 21.1 1.0
OD1 A:ASP564 1.9 24.3 1.0
O A:HOH907 2.0 19.7 1.0
O A:HOH977 2.0 25.0 1.0
O A:HOH945 2.1 25.9 1.0
O A:HOH946 2.2 25.1 1.0
CG A:ASP564 3.0 23.9 1.0
OD2 A:ASP564 3.3 24.6 1.0
O A:HOH1026 3.7 37.6 1.0
ZN A:ZN801 3.7 30.2 1.0
O A:HOH971 4.0 34.0 1.0
OE2 A:GLU592 4.0 31.2 1.0
NE2 A:HIS595 4.1 26.6 1.0
OG1 A:THR633 4.2 24.9 1.0
CD2 A:HIS563 4.2 21.1 1.0
CD2 A:HIS567 4.3 29.1 1.0
O A:HIS563 4.3 26.9 1.0
CD2 A:HIS595 4.3 29.1 1.0
CB A:ASP564 4.4 22.9 1.0
O A:HOH991 4.4 33.8 1.0
OD2 A:ASP674 4.5 36.5 1.0
NE2 A:HIS567 4.5 27.2 1.0
O A:THR633 4.5 28.0 1.0
CD2 A:HIS525 4.6 25.3 1.0
NE2 A:HIS563 4.6 23.9 1.0
NE2 A:HIS525 4.6 31.3 1.0
CB A:THR633 4.7 26.9 1.0
CA A:ASP564 4.8 23.0 1.0
CD A:GLU592 4.9 25.6 1.0
CG A:GLU592 4.9 27.4 1.0

Magnesium binding site 2 out of 4 in 5sfr

Go back to Magnesium Binding Sites List in 5sfr
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide


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-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:22.8
occ:1.00
 O B:HOH918 1.9 27.1 1.0
O B:HOH1018 2.0 25.4 1.0
OD1 B:ASP564 2.1 25.7 1.0
O B:HOH954 2.1 24.5 1.0
O B:HOH906 2.1 20.9 1.0
O B:HOH971 2.2 22.2 1.0
CG B:ASP564 3.1 26.7 1.0
OD2 B:ASP564 3.4 24.2 1.0
O B:HOH962 3.8 38.3 1.0
ZN B:ZN801 3.8 28.7 1.0
O B:HOH1039 3.9 32.5 1.0
NE2 B:HIS595 4.2 23.8 1.0
CD2 B:HIS563 4.2 21.6 1.0
O B:HOH982 4.2 28.5 1.0
OG1 B:THR633 4.2 26.4 1.0
OE2 B:GLU592 4.2 28.6 1.0
CD2 B:HIS567 4.3 24.6 1.0
OD2 B:ASP674 4.3 30.5 1.0
O B:HIS563 4.4 31.2 1.0
NE2 B:HIS567 4.4 26.2 1.0
CD2 B:HIS595 4.4 27.8 1.0
CB B:ASP564 4.4 26.4 1.0
NE2 B:HIS563 4.5 24.4 1.0
CD2 B:HIS525 4.6 26.7 1.0
NE2 B:HIS525 4.6 25.0 1.0
O B:THR633 4.6 23.9 1.0
CB B:THR633 4.7 24.3 1.0
CA B:ASP564 4.8 24.2 1.0
CG B:GLU592 4.8 25.3 1.0
CD B:GLU592 4.9 26.3 1.0

Magnesium binding site 3 out of 4 in 5sfr

Go back to Magnesium Binding Sites List in 5sfr
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide


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-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:24.8
occ:1.00
 OD1 C:ASP564 2.1 25.4 1.0
O C:HOH944 2.1 23.2 1.0
O C:HOH917 2.1 28.5 1.0
O C:HOH993 2.1 25.0 1.0
O C:HOH998 2.1 23.5 1.0
O C:HOH921 2.2 24.1 1.0
CG C:ASP564 3.1 29.7 1.0
OD2 C:ASP564 3.4 25.7 1.0
ZN C:ZN801 3.7 31.4 1.0
O C:HOH1050 3.8 47.2 1.0
O C:HOH992 3.9 36.2 1.0
CD2 C:HIS563 4.1 24.9 1.0
OE2 C:GLU592 4.1 29.6 1.0
OG1 C:THR633 4.2 26.5 1.0
NE2 C:HIS595 4.2 28.6 1.0
OD2 C:ASP674 4.3 37.5 1.0
CD2 C:HIS567 4.3 26.3 1.0
O C:HOH999 4.3 31.9 1.0
O C:HIS563 4.4 27.1 1.0
O C:THR633 4.4 31.3 1.0
CD2 C:HIS595 4.4 24.8 1.0
CB C:ASP564 4.5 25.2 1.0
NE2 C:HIS563 4.5 28.0 1.0
NE2 C:HIS567 4.5 23.4 1.0
CD2 C:HIS525 4.6 25.8 1.0
NE2 C:HIS525 4.6 27.0 1.0
CB C:THR633 4.7 27.9 1.0
CG C:GLU592 4.8 26.6 1.0
CA C:ASP564 4.8 28.5 1.0
CD C:GLU592 4.9 27.5 1.0
OD1 C:ASP674 5.0 24.4 1.0

Magnesium binding site 4 out of 4 in 5sfr

Go back to Magnesium Binding Sites List in 5sfr
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide


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-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:30.7
occ:1.00
 O D:HOH975 2.0 29.1 1.0
O D:HOH956 2.1 29.3 1.0
O D:HOH922 2.1 27.9 1.0
O D:HOH951 2.1 26.9 1.0
O D:HOH908 2.2 26.5 1.0
OD1 D:ASP564 2.2 30.5 1.0
CG D:ASP564 3.2 28.6 1.0
OD2 D:ASP564 3.5 29.6 1.0
ZN D:ZN801 3.9 35.8 1.0
OE2 D:GLU592 4.0 34.6 1.0
NE2 D:HIS595 4.0 34.8 1.0
O D:HOH967 4.1 37.0 1.0
OG1 D:THR633 4.2 36.5 1.0
CD2 D:HIS567 4.3 38.2 1.0
O D:HOH965 4.3 37.9 1.0
CD2 D:HIS563 4.3 28.7 1.0
CD2 D:HIS595 4.4 33.7 1.0
O D:HIS563 4.4 33.6 1.0
NE2 D:HIS567 4.5 33.0 1.0
OD2 D:ASP674 4.5 39.2 1.0
O D:THR633 4.5 33.3 1.0
CD2 D:HIS525 4.5 34.2 1.0
CB D:ASP564 4.5 28.2 1.0
NE2 D:HIS525 4.6 38.6 1.0
NE2 D:HIS563 4.7 26.8 1.0
CB D:THR633 4.7 35.2 1.0
CD D:GLU592 4.9 38.4 1.0
CA D:ASP564 4.9 29.1 1.0
CG D:GLU592 5.0 36.6 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 19:31:52 2025

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