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

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

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-6- (Trifluoromethyl)-[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 2-[2- (2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-6- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-A]Pyridine, PDB code: 5seu 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) 43.49 / 2.09
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.19, 135.19, 235.047, 90, 90, 120
R / Rfree (%) 18.3 / 23.8

Other elements in 5seu:

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

Fluorine (F) 18 atoms
Zinc (Zn) 4 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 5seu

Go back to Magnesium Binding Sites List in 5seu
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-6- (Trifluoromethyl)-[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 2-[2- (2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-6- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:33.7
occ:1.00
 O A:HOH970 2.0 33.8 1.0
O A:HOH966 2.0 25.1 1.0
OD1 A:ASP564 2.0 30.2 1.0
O A:HOH917 2.1 25.3 1.0
O A:HOH945 2.2 27.7 1.0
O A:HOH931 2.2 31.6 1.0
CG A:ASP564 3.1 34.0 1.0
OD2 A:ASP564 3.5 32.3 1.0
ZN A:ZN801 3.7 37.0 1.0
O A:HOH964 3.8 35.8 1.0
NE2 A:HIS595 4.0 30.0 1.0
O A:HOH946 4.0 33.7 1.0
OE2 A:GLU592 4.0 40.2 1.0
OG1 A:THR633 4.3 34.8 1.0
CD2 A:HIS567 4.3 35.4 1.0
CD2 A:HIS595 4.3 30.2 1.0
CD2 A:HIS563 4.3 32.9 1.0
O A:HIS563 4.4 32.6 1.0
CB A:ASP564 4.4 28.8 1.0
CD2 A:HIS525 4.5 33.6 1.0
NE2 A:HIS525 4.5 38.4 1.0
NE2 A:HIS567 4.5 33.1 1.0
O A:THR633 4.5 28.9 1.0
OD2 A:ASP674 4.7 39.8 1.0
CB A:THR633 4.7 32.3 1.0
NE2 A:HIS563 4.7 30.1 1.0
CA A:ASP564 4.8 31.2 1.0
CG A:GLU592 4.8 32.6 1.0
CD A:GLU592 4.9 37.3 1.0

Magnesium binding site 2 out of 4 in 5seu

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-6- (Trifluoromethyl)-[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 2-[2- (2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-6- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:30.7
occ:1.00
 O B:HOH947 2.0 28.1 1.0
O B:HOH960 2.1 26.8 1.0
O B:HOH925 2.1 29.5 1.0
O B:HOH909 2.1 26.7 1.0
O B:HOH974 2.1 26.1 1.0
OD1 B:ASP564 2.2 31.4 1.0
CG B:ASP564 3.2 27.8 1.0
O B:HOH993 3.6 48.5 1.0
OD2 B:ASP564 3.6 33.5 1.0
ZN B:ZN801 3.8 34.8 1.0
O B:HOH961 3.8 38.4 1.0
OE2 B:GLU592 4.0 32.8 1.0
O B:HOH936 4.0 30.7 1.0
NE2 B:HIS595 4.1 28.9 1.0
OG1 B:THR633 4.1 27.8 1.0
CD2 B:HIS563 4.3 28.3 1.0
CD2 B:HIS567 4.3 30.2 1.0
NE2 B:HIS567 4.4 27.5 1.0
O B:HIS563 4.4 33.8 1.0
CD2 B:HIS595 4.4 34.5 1.0
OD2 B:ASP674 4.4 32.1 1.0
O B:THR633 4.4 30.4 1.0
CB B:ASP564 4.5 27.4 1.0
NE2 B:HIS563 4.6 27.2 1.0
CB B:THR633 4.7 28.1 1.0
CD2 B:HIS525 4.7 31.9 1.0
NE2 B:HIS525 4.7 34.3 1.0
CG B:GLU592 4.7 30.6 1.0
CD B:GLU592 4.8 30.9 1.0
CA B:ASP564 4.8 28.9 1.0

Magnesium binding site 3 out of 4 in 5seu

Go back to Magnesium Binding Sites List in 5seu
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-6- (Trifluoromethyl)-[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 2-[2- (2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-6- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:33.1
occ:1.00
 O C:HOH960 2.0 30.2 1.0
O C:HOH942 2.0 33.8 1.0
OD1 C:ASP564 2.1 31.4 1.0
O C:HOH917 2.1 26.3 1.0
O C:HOH919 2.1 28.0 1.0
O C:HOH988 2.2 28.0 1.0
CG C:ASP564 3.1 31.0 1.0
OD2 C:ASP564 3.5 30.9 1.0
ZN C:ZN801 3.8 36.9 1.0
O C:HOH991 3.8 42.5 1.0
OE2 C:GLU592 3.9 38.2 1.0
NE2 C:HIS595 3.9 37.0 1.0
O C:HOH941 4.0 40.7 1.0
CD2 C:HIS567 4.2 30.2 1.0
OG1 C:THR633 4.2 32.1 1.0
CD2 C:HIS563 4.2 27.2 1.0
O C:HOH939 4.2 34.3 1.0
O C:HIS563 4.3 30.5 1.0
CD2 C:HIS595 4.3 35.5 1.0
OD2 C:ASP674 4.4 33.9 1.0
CB C:ASP564 4.4 29.5 1.0
NE2 C:HIS567 4.4 32.7 1.0
O C:THR633 4.5 31.9 1.0
CB C:THR633 4.6 31.6 1.0
NE2 C:HIS563 4.7 31.1 1.0
CG C:GLU592 4.7 33.1 1.0
CA C:ASP564 4.7 32.7 1.0
CD C:GLU592 4.7 34.7 1.0
CD2 C:HIS525 4.7 30.7 1.0
NE2 C:HIS525 4.8 34.0 1.0

Magnesium binding site 4 out of 4 in 5seu

Go back to Magnesium Binding Sites List in 5seu
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-6- (Trifluoromethyl)-[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 2-[2- (2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-6- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:48.2
occ:1.00
 OD1 D:ASP564 2.0 48.7 1.0
O D:HOH921 2.1 42.3 1.0
O D:HOH924 2.1 37.8 1.0
O D:HOH915 2.2 37.6 1.0
O D:HOH908 2.2 38.2 1.0
O D:HOH901 2.3 46.3 1.0
CG D:ASP564 3.0 47.3 1.0
OD2 D:ASP564 3.3 57.4 1.0
O D:HOH922 3.5 43.2 1.0
O D:HOH923 3.6 47.5 1.0
ZN D:ZN801 3.7 53.6 1.0
NE2 D:HIS595 3.9 50.2 1.0
CD2 D:HIS567 4.1 47.8 1.0
OE2 D:GLU592 4.1 49.0 1.0
CD2 D:HIS595 4.3 55.7 1.0
CD2 D:HIS563 4.3 46.1 1.0
NE2 D:HIS567 4.3 49.1 1.0
CB D:ASP564 4.3 46.7 1.0
OG1 D:THR633 4.3 45.9 1.0
O D:HIS563 4.3 42.1 1.0
CD2 D:HIS525 4.4 48.3 1.0
NE2 D:HIS525 4.5 53.8 1.0
CA D:ASP564 4.6 42.2 1.0
O D:THR633 4.6 49.3 1.0
NE2 D:HIS563 4.7 43.9 1.0
OD2 D:ASP674 4.7 50.8 1.0
CB D:THR633 4.9 53.6 1.0
CE1 D:HIS595 4.9 51.8 1.0
CD D:GLU592 4.9 55.4 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 03:27:16 2024

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