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Magnesium in PDB 5sej: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine, PDB code: 5sej 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) 43.62 / 2.44
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.506, 135.506, 234.911, 90, 90, 120
R / Rfree (%) 17.4 / 24.3

Other elements in 5sej:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine (pdb code 5sej). 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 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine, PDB code: 5sej:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sej

Go back to Magnesium Binding Sites List in 5sej
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine


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

b:44.8
occ:1.00
 O A:HOH948 1.9 28.3 1.0
O A:HOH905 2.0 32.5 1.0
O A:HOH924 2.1 43.4 1.0
O A:HOH904 2.1 40.9 1.0
O A:HOH933 2.1 39.0 1.0
OD1 A:ASP564 2.1 37.6 1.0
CG A:ASP564 3.1 34.5 1.0
OD2 A:ASP564 3.4 40.2 1.0
OE2 A:GLU592 3.7 49.4 1.0
ZN A:ZN801 3.9 49.6 1.0
O A:HOH915 3.9 39.3 1.0
NE2 A:HIS595 4.0 39.1 1.0
O A:HOH919 4.0 42.0 1.0
CD2 A:HIS567 4.2 40.6 1.0
OG1 A:THR633 4.3 41.3 1.0
CD2 A:HIS595 4.3 41.1 1.0
O A:THR633 4.4 38.9 1.0
O A:HIS563 4.4 41.7 1.0
CB A:ASP564 4.5 32.5 1.0
NE2 A:HIS567 4.5 41.8 1.0
NE2 A:HIS525 4.6 45.1 1.0
CD2 A:HIS563 4.6 38.6 1.0
CD2 A:HIS525 4.6 46.2 1.0
CD A:GLU592 4.7 45.1 1.0
OD2 A:ASP674 4.7 41.9 1.0
CB A:THR633 4.8 37.6 1.0
NE2 A:HIS563 4.8 38.2 1.0
CA A:ASP564 4.8 35.6 1.0
CG A:GLU592 4.9 40.1 1.0

Magnesium binding site 2 out of 4 in 5sej

Go back to Magnesium Binding Sites List in 5sej
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine


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

b:32.1
occ:1.00
 O B:HOH935 1.9 29.4 1.0
O B:HOH949 2.0 27.0 1.0
O B:HOH920 2.0 28.4 1.0
OD1 B:ASP564 2.1 35.9 1.0
O B:HOH904 2.1 25.5 1.0
O B:HOH922 2.1 29.6 1.0
CG B:ASP564 3.1 39.2 1.0
OD2 B:ASP564 3.5 41.7 1.0
ZN B:ZN801 3.8 42.4 1.0
OE2 B:GLU592 4.0 36.6 1.0
OG1 B:THR633 4.0 37.7 1.0
O B:HOH914 4.0 36.7 1.0
NE2 B:HIS595 4.0 38.1 1.0
CD2 B:HIS563 4.1 34.9 1.0
CD2 B:HIS595 4.3 40.6 1.0
O B:HIS563 4.4 40.6 1.0
CD2 B:HIS567 4.4 41.6 1.0
OD2 B:ASP674 4.4 41.6 1.0
CB B:ASP564 4.5 35.7 1.0
NE2 B:HIS563 4.5 31.5 1.0
CD2 B:HIS525 4.6 41.5 1.0
O B:THR633 4.6 28.4 1.0
NE2 B:HIS567 4.6 39.2 1.0
CB B:THR633 4.6 40.3 1.0
NE2 B:HIS525 4.7 37.9 1.0
CA B:ASP564 4.8 39.9 1.0
CG B:GLU592 4.8 36.2 1.0
CD B:GLU592 4.8 36.3 1.0

Magnesium binding site 3 out of 4 in 5sej

Go back to Magnesium Binding Sites List in 5sej
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine


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

b:36.4
occ:1.00
 OD1 C:ASP564 2.0 34.2 1.0
O C:HOH919 2.0 35.0 1.0
O C:HOH933 2.0 30.5 1.0
O C:HOH935 2.0 33.0 1.0
O C:HOH911 2.2 28.1 1.0
O C:HOH952 2.3 39.6 1.0
CG C:ASP564 2.9 33.5 1.0
OD2 C:ASP564 3.2 40.3 1.0
ZN C:ZN801 3.6 45.2 1.0
O C:HOH972 3.7 47.8 1.0
NE2 C:HIS595 4.0 39.3 1.0
CD2 C:HIS563 4.1 35.5 1.0
OE2 C:GLU592 4.2 42.3 1.0
O C:HIS563 4.2 40.2 1.0
CD2 C:HIS595 4.2 37.9 1.0
CB C:ASP564 4.3 35.2 1.0
CD2 C:HIS567 4.3 43.0 1.0
OG1 C:THR633 4.4 37.6 1.0
OD2 C:ASP674 4.4 38.1 1.0
O C:HOH930 4.4 33.4 1.0
O C:THR633 4.4 41.7 1.0
NE2 C:HIS563 4.5 38.2 1.0
NE2 C:HIS567 4.5 42.6 1.0
CB C:THR633 4.6 38.7 1.0
CA C:ASP564 4.7 37.2 1.0
CD2 C:HIS525 4.7 42.0 1.0
NE2 C:HIS525 4.7 48.2 1.0
CG C:GLU592 4.8 44.0 1.0
C C:HIS563 4.9 39.4 1.0
CD C:GLU592 5.0 44.3 1.0

Magnesium binding site 4 out of 4 in 5sej

Go back to Magnesium Binding Sites List in 5sej
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine


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

b:56.5
occ:1.00
 O D:HOH925 2.1 47.4 1.0
O D:HOH903 2.2 44.1 1.0
O D:HOH912 2.2 48.6 1.0
OD1 D:ASP564 2.3 57.2 1.0
O D:HOH901 2.4 58.9 1.0
CG D:ASP564 3.1 57.4 1.0
OD2 D:ASP564 3.4 71.3 1.0
O D:HOH917 3.5 44.5 1.0
O D:HOH916 3.8 45.0 1.0
ZN D:ZN801 3.8 63.7 1.0
OE2 D:GLU592 3.9 54.4 1.0
NE2 D:HIS595 4.1 64.9 1.0
CD2 D:HIS567 4.3 50.5 1.0
OG1 D:THR633 4.3 60.0 1.0
CD2 D:HIS595 4.4 60.1 1.0
O D:HIS563 4.4 56.8 1.0
CD2 D:HIS563 4.5 57.8 1.0
CB D:ASP564 4.5 54.3 1.0
NE2 D:HIS567 4.6 58.5 1.0
O D:THR633 4.6 57.7 1.0
OD2 D:ASP674 4.6 61.7 1.0
NE2 D:HIS525 4.7 59.1 1.0
CD2 D:HIS525 4.7 62.9 1.0
CB D:THR633 4.7 61.7 1.0
CD D:GLU592 4.8 57.7 1.0
CA D:ASP564 4.9 56.8 1.0
NE2 D:HIS563 4.9 49.2 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 03:23:04 2024

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