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

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[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-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[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-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyridine, PDB code: 5sei 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) 43.50 / 2.37
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.211, 135.211, 235.374, 90, 90, 120
R / Rfree (%) 17.2 / 23.5

Other elements in 5sei:

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

Magnesium binding site 1 out of 4 in 5sei

Go back to Magnesium Binding Sites List in 5sei
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[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-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:36.3
occ:1.00
 O A:HOH981 1.9 32.0 1.0
OD1 A:ASP564 1.9 40.3 1.0
O A:HOH910 2.0 27.4 1.0
O A:HOH921 2.1 32.4 1.0
O A:HOH938 2.1 33.5 1.0
O A:HOH922 2.2 35.5 1.0
CG A:ASP564 2.9 37.6 1.0
OD2 A:ASP564 3.2 42.5 1.0
ZN A:ZN802 3.8 41.5 1.0
O A:HOH914 3.9 34.0 1.0
NE2 A:HIS595 4.0 32.9 1.0
OE2 A:GLU592 4.1 40.8 1.0
O A:HIS563 4.2 32.0 1.0
O A:HOH931 4.2 39.1 1.0
OG1 A:THR633 4.2 39.7 1.0
CD2 A:HIS563 4.2 31.4 1.0
CD2 A:HIS567 4.2 39.8 1.0
CD2 A:HIS595 4.3 34.7 1.0
CB A:ASP564 4.3 33.8 1.0
NE2 A:HIS567 4.5 40.8 1.0
O A:THR633 4.5 36.0 1.0
CD2 A:HIS525 4.5 35.8 1.0
NE2 A:HIS525 4.6 38.1 1.0
NE2 A:HIS563 4.6 28.5 1.0
OD2 A:ASP674 4.7 46.4 1.0
CA A:ASP564 4.7 34.0 1.0
CB A:THR633 4.7 34.0 1.0
CG A:GLU592 4.8 36.9 1.0
CD A:GLU592 4.9 40.6 1.0
C A:HIS563 5.0 31.7 1.0

Magnesium binding site 2 out of 4 in 5sei

Go back to Magnesium Binding Sites List in 5sei
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[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-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:30.5
occ:1.00
 O B:HOH964 1.9 33.9 1.0
O B:HOH943 1.9 35.0 1.0
O B:HOH912 2.0 22.5 1.0
OD1 B:ASP564 2.1 32.4 1.0
O B:HOH952 2.2 26.5 1.0
O B:HOH959 2.2 27.7 1.0
CG B:ASP564 3.1 33.9 1.0
OD2 B:ASP564 3.4 37.9 1.0
ZN B:ZN802 3.7 39.9 1.0
OE2 B:GLU592 4.1 37.1 1.0
CD2 B:HIS563 4.1 34.3 1.0
OG1 B:THR633 4.1 34.5 1.0
NE2 B:HIS595 4.1 36.3 1.0
O B:HOH929 4.2 36.3 1.0
O B:HIS563 4.3 39.0 1.0
CD2 B:HIS567 4.4 39.4 1.0
O B:THR633 4.4 32.1 1.0
CD2 B:HIS595 4.4 37.8 1.0
OD2 B:ASP674 4.4 37.6 1.0
CB B:ASP564 4.4 32.5 1.0
NE2 B:HIS567 4.5 38.6 1.0
NE2 B:HIS563 4.5 30.8 1.0
CD2 B:HIS525 4.6 37.6 1.0
CB B:THR633 4.6 34.5 1.0
NE2 B:HIS525 4.7 34.4 1.0
CA B:ASP564 4.8 35.8 1.0
CG B:GLU592 4.8 36.4 1.0
CD B:GLU592 4.9 38.1 1.0

Magnesium binding site 3 out of 4 in 5sei

Go back to Magnesium Binding Sites List in 5sei
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[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-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg803

b:31.2
occ:1.00
 O C:HOH936 1.9 34.6 1.0
O C:HOH969 2.0 28.2 1.0
O C:HOH949 2.0 24.9 1.0
OD1 C:ASP564 2.0 36.4 1.0
O C:HOH940 2.2 27.2 1.0
O C:HOH987 2.2 33.2 1.0
CG C:ASP564 3.0 34.1 1.0
OD2 C:ASP564 3.3 34.7 1.0
O C:HOH976 3.8 44.9 1.0
ZN C:ZN802 3.8 40.5 1.0
O C:HOH908 3.9 39.8 1.0
NE2 C:HIS595 4.0 41.6 1.0
OE2 C:GLU592 4.1 38.4 1.0
CD2 C:HIS563 4.1 34.2 1.0
CD2 C:HIS567 4.2 39.3 1.0
OG1 C:THR633 4.2 34.5 1.0
O C:HIS563 4.3 34.6 1.0
CD2 C:HIS595 4.3 39.5 1.0
O C:HOH948 4.3 37.6 1.0
CB C:ASP564 4.4 33.6 1.0
NE2 C:HIS567 4.5 44.2 1.0
OD2 C:ASP674 4.5 36.6 1.0
NE2 C:HIS563 4.5 34.5 1.0
O C:THR633 4.6 35.6 1.0
CB C:THR633 4.6 35.2 1.0
NE2 C:HIS525 4.7 36.7 1.0
CD2 C:HIS525 4.7 36.1 1.0
CA C:ASP564 4.8 35.1 1.0
CG C:GLU592 4.8 38.9 1.0
CD C:GLU592 4.9 40.8 1.0

Magnesium binding site 4 out of 4 in 5sei

Go back to Magnesium Binding Sites List in 5sei
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[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-[(E)-2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg803

b:52.5
occ:1.00
 O D:HOH933 2.0 36.3 1.0
O D:HOH928 2.0 41.1 1.0
OD1 D:ASP564 2.1 46.5 1.0
O D:HOH926 2.2 47.4 1.0
O D:HOH907 2.2 48.2 1.0
O D:HOH902 2.3 44.3 1.0
CG D:ASP564 3.0 53.0 1.0
OD2 D:ASP564 3.4 63.4 1.0
O D:HOH920 3.7 46.6 1.0
ZN D:ZN802 3.8 57.0 1.0
OE2 D:GLU592 3.9 50.5 1.0
O D:HOH915 4.0 58.9 1.0
NE2 D:HIS595 4.0 54.8 1.0
CD2 D:HIS567 4.2 53.9 1.0
CD2 D:HIS563 4.3 49.1 1.0
CD2 D:HIS595 4.3 57.3 1.0
OG1 D:THR633 4.3 50.8 1.0
O D:HIS563 4.3 54.9 1.0
CB D:ASP564 4.4 51.1 1.0
O D:THR633 4.5 54.5 1.0
NE2 D:HIS567 4.5 54.0 1.0
OD2 D:ASP674 4.5 55.8 1.0
CD2 D:HIS525 4.6 62.1 1.0
NE2 D:HIS525 4.7 60.6 1.0
NE2 D:HIS563 4.7 43.3 1.0
CA D:ASP564 4.7 47.5 1.0
CB D:THR633 4.8 55.7 1.0
CD D:GLU592 4.8 50.5 1.0
CG D:GLU592 4.9 53.8 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 03:22:58 2024

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