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Magnesium in PDB 5sfw: Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Ethyl-8-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine

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

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

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Ethyl-8-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, PDB code: 5sfw was solved by C.Joseph, C.Lerner, 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) 43.65 / 2.15
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.144, 135.144, 235.212, 90, 90, 120
R / Rfree (%) 18.2 / 24.1

Other elements in 5sfw:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Ethyl-8-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine 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- Ethyl-8-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine (pdb code 5sfw). 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- Ethyl-8-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, PDB code: 5sfw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sfw

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


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- Ethyl-8-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:33.5
occ:1.00
 O A:HOH954 1.9 35.4 1.0
OD1 A:ASP564 1.9 33.2 1.0
O A:HOH942 2.0 36.5 1.0
O A:HOH973 2.0 29.5 1.0
O A:HOH933 2.0 28.1 1.0
O A:HOH931 2.1 29.5 1.0
CG A:ASP564 3.0 31.0 1.0
OD2 A:ASP564 3.4 37.5 1.0
ZN A:ZN801 3.8 40.3 1.0
O A:HOH922 3.9 46.2 1.0
NE2 A:HIS595 3.9 36.1 1.0
OE2 A:GLU592 4.0 38.7 1.0
O A:HOH1000 4.1 60.1 1.0
O A:HOH934 4.1 38.8 1.0
O A:HIS563 4.3 35.5 1.0
CD2 A:HIS567 4.3 30.7 1.0
CB A:ASP564 4.3 30.4 1.0
OG1 A:THR633 4.3 38.9 1.0
CD2 A:HIS595 4.3 31.2 1.0
CD2 A:HIS563 4.4 36.7 1.0
CD2 A:HIS525 4.5 37.3 1.0
NE2 A:HIS525 4.5 38.0 1.0
O A:THR633 4.6 35.4 1.0
NE2 A:HIS567 4.6 31.3 1.0
CA A:ASP564 4.7 31.9 1.0
OD2 A:ASP674 4.7 46.0 1.0
CB A:THR633 4.7 34.4 1.0
NE2 A:HIS563 4.8 32.6 1.0
CD A:GLU592 4.8 41.4 1.0
CG A:GLU592 4.9 36.5 1.0
CE1 A:HIS595 5.0 34.3 1.0

Magnesium binding site 2 out of 4 in 5sfw

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


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- Ethyl-8-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:32.4
occ:1.00
 O B:HOH948 1.8 29.9 1.0
O B:HOH944 2.0 40.0 1.0
O B:HOH968 2.1 25.9 1.0
OD1 B:ASP564 2.1 37.7 1.0
O B:HOH955 2.2 32.6 1.0
O B:HOH904 2.2 27.2 1.0
CG B:ASP564 3.1 31.2 1.0
OD2 B:ASP564 3.5 41.7 1.0
ZN B:ZN801 3.7 39.0 1.0
O B:HOH915 4.0 42.7 1.0
OE2 B:GLU592 4.1 36.7 1.0
NE2 B:HIS595 4.1 34.9 1.0
O B:HOH952 4.2 40.6 1.0
OG1 B:THR633 4.2 30.6 1.0
CD2 B:HIS563 4.3 30.9 1.0
O B:HIS563 4.3 36.4 1.0
CD2 B:HIS567 4.4 34.5 1.0
CD2 B:HIS595 4.4 36.4 1.0
OD2 B:ASP674 4.4 35.7 1.0
CD2 B:HIS525 4.5 37.1 1.0
CB B:ASP564 4.5 33.6 1.0
NE2 B:HIS567 4.5 32.8 1.0
O B:THR633 4.6 38.2 1.0
NE2 B:HIS525 4.6 41.2 1.0
NE2 B:HIS563 4.6 29.2 1.0
CB B:THR633 4.7 32.2 1.0
CG B:GLU592 4.8 40.5 1.0
CA B:ASP564 4.8 36.0 1.0
CD B:GLU592 4.9 38.3 1.0

Magnesium binding site 3 out of 4 in 5sfw

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


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- Ethyl-8-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:32.4
occ:1.00
 O C:HOH931 1.9 26.2 1.0
OD1 C:ASP564 2.0 37.0 1.0
O C:HOH938 2.0 32.8 1.0
O C:HOH960 2.1 26.9 1.0
O C:HOH970 2.1 34.5 1.0
O C:HOH993 2.2 29.1 1.0
CG C:ASP564 3.0 33.5 1.0
OD2 C:ASP564 3.4 36.9 1.0
ZN C:ZN801 3.7 39.9 1.0
OE2 C:GLU592 4.0 33.4 1.0
NE2 C:HIS595 4.0 35.9 1.0
O C:HOH956 4.0 57.6 1.0
O C:HOH963 4.2 36.0 1.0
CD2 C:HIS567 4.2 34.6 1.0
OG1 C:THR633 4.3 35.7 1.0
O C:HIS563 4.3 31.6 1.0
CD2 C:HIS563 4.3 29.1 1.0
CD2 C:HIS595 4.3 37.3 1.0
CB C:ASP564 4.4 30.4 1.0
NE2 C:HIS567 4.4 31.5 1.0
OD2 C:ASP674 4.4 33.6 1.0
O C:THR633 4.5 37.5 1.0
CD2 C:HIS525 4.6 37.8 1.0
CB C:THR633 4.6 36.1 1.0
NE2 C:HIS525 4.6 41.4 1.0
NE2 C:HIS563 4.7 30.7 1.0
CA C:ASP564 4.7 35.5 1.0
CG C:GLU592 4.8 34.7 1.0
CD C:GLU592 4.8 35.4 1.0

Magnesium binding site 4 out of 4 in 5sfw

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


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- Ethyl-8-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:52.0
occ:1.00
 O D:HOH927 2.0 40.2 1.0
O D:HOH905 2.0 49.4 1.0
O D:HOH938 2.0 43.1 1.0
O D:HOH923 2.1 42.4 1.0
OD1 D:ASP564 2.2 52.9 1.0
O D:HOH912 2.3 50.2 1.0
CG D:ASP564 3.2 46.8 1.0
OD2 D:ASP564 3.4 57.0 1.0
O D:HOH940 3.8 43.9 1.0
O D:HOH916 3.8 50.5 1.0
ZN D:ZN801 3.8 53.5 1.0
OE2 D:GLU592 3.9 51.4 1.0
NE2 D:HIS595 4.0 57.8 1.0
CD2 D:HIS567 4.2 53.4 1.0
CD2 D:HIS595 4.4 62.2 1.0
O D:HIS563 4.4 49.4 1.0
NE2 D:HIS567 4.4 53.2 1.0
OG1 D:THR633 4.5 48.0 1.0
CD2 D:HIS563 4.5 43.6 1.0
NE2 D:HIS525 4.5 56.7 1.0
CB D:ASP564 4.5 46.6 1.0
OD2 D:ASP674 4.5 58.7 1.0
CD2 D:HIS525 4.6 49.0 1.0
O D:THR633 4.7 60.5 1.0
CD D:GLU592 4.8 58.1 1.0
CB D:THR633 4.8 47.9 1.0
NE2 D:HIS563 4.8 40.6 1.0
CA D:ASP564 4.8 48.5 1.0
CG D:GLU592 5.0 53.2 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: Mon Sep 30 03:40:50 2024

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