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Magnesium in PDB 5se8: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(2-Methyl-5-Phenyl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(2-Methyl-5-Phenyl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(2-Methyl-5-Phenyl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(2-Methyl-5-Phenyl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide, PDB code: 5se8 was solved by C.Joseph, M.Koerner, 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) 43.69 / 1.99
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.812, 135.812, 235.994, 90, 90, 120
R / Rfree (%) 17.3 / 21.7

Other elements in 5se8:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(2-Methyl-5-Phenyl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide 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 4- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(2-Methyl-5-Phenyl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide (pdb code 5se8). 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- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(2-Methyl-5-Phenyl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide, PDB code: 5se8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5se8

Go back to Magnesium Binding Sites List in 5se8
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(2-Methyl-5-Phenyl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide


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- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(2-Methyl-5-Phenyl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:24.6
occ:1.00
 O A:HOH980 2.0 21.7 1.0
O A:HOH997 2.0 22.8 1.0
OD1 A:ASP564 2.0 22.5 1.0
O A:HOH953 2.0 20.1 1.0
O A:HOH944 2.1 19.9 1.0
O A:HOH960 2.2 23.3 1.0
CG A:ASP564 3.1 22.4 1.0
OD2 A:ASP564 3.5 22.5 1.0
ZN A:ZN801 3.7 28.7 1.0
O A:HOH1021 4.0 32.1 1.0
OE2 A:GLU592 4.0 26.8 1.0
NE2 A:HIS595 4.1 24.8 1.0
O A:HOH966 4.3 32.8 1.0
CD2 A:HIS567 4.3 27.0 1.0
O A:HIS563 4.3 26.4 1.0
OG1 A:THR633 4.3 24.8 1.0
CD2 A:HIS595 4.4 24.4 1.0
O A:HOH1030 4.4 50.6 1.0
CD2 A:HIS563 4.4 22.5 1.0
CB A:ASP564 4.4 22.7 1.0
NE2 A:HIS567 4.4 26.4 1.0
NE2 A:HIS525 4.5 28.3 1.0
O A:THR633 4.5 26.9 1.0
CD2 A:HIS525 4.6 30.2 1.0
OD2 A:ASP674 4.6 30.0 1.0
CB A:THR633 4.7 25.3 1.0
NE2 A:HIS563 4.8 23.6 1.0
CG A:GLU592 4.8 24.7 1.0
CA A:ASP564 4.8 23.2 1.0
CD A:GLU592 4.8 26.9 1.0

Magnesium binding site 2 out of 4 in 5se8

Go back to Magnesium Binding Sites List in 5se8
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(2-Methyl-5-Phenyl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide


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- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(2-Methyl-5-Phenyl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:23.0
occ:1.00
 O B:HOH991 1.9 21.3 1.0
O B:HOH943 2.0 21.9 1.0
OD1 B:ASP564 2.0 22.7 1.0
O B:HOH970 2.1 21.6 1.0
O B:HOH999 2.1 20.6 1.0
O B:HOH914 2.1 19.8 1.0
CG B:ASP564 3.1 21.3 1.0
OD2 B:ASP564 3.5 20.7 1.0
ZN B:ZN801 3.8 27.9 1.0
O B:HOH1004 4.0 35.0 1.0
OE2 B:GLU592 4.1 26.2 1.0
NE2 B:HIS595 4.1 21.1 1.0
OG1 B:THR633 4.2 25.6 1.0
O B:HOH973 4.2 30.1 1.0
CD2 B:HIS567 4.3 23.2 1.0
CD2 B:HIS563 4.3 20.4 1.0
O B:HIS563 4.3 22.7 1.0
CD2 B:HIS595 4.4 22.8 1.0
OD2 B:ASP674 4.4 24.4 1.0
CB B:ASP564 4.4 20.6 1.0
NE2 B:HIS567 4.5 24.1 1.0
O B:THR633 4.5 23.7 1.0
CD2 B:HIS525 4.5 22.9 1.0
NE2 B:HIS525 4.6 26.2 1.0
NE2 B:HIS563 4.7 19.9 1.0
CB B:THR633 4.7 24.1 1.0
CG B:GLU592 4.8 24.5 1.0
CA B:ASP564 4.8 21.8 1.0
CD B:GLU592 4.8 26.1 1.0

Magnesium binding site 3 out of 4 in 5se8

Go back to Magnesium Binding Sites List in 5se8
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(2-Methyl-5-Phenyl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide


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- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(2-Methyl-5-Phenyl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:24.0
occ:1.00
 O C:HOH956 2.0 25.2 1.0
O C:HOH958 2.0 21.3 1.0
O C:HOH974 2.0 22.5 1.0
OD1 C:ASP564 2.1 21.7 1.0
O C:HOH1036 2.1 24.8 1.0
O C:HOH943 2.2 20.4 1.0
CG C:ASP564 3.0 23.4 1.0
OD2 C:ASP564 3.4 26.5 1.0
ZN C:ZN801 3.7 29.9 1.0
O C:HOH1016 3.9 31.1 1.0
NE2 C:HIS595 4.0 24.9 1.0
OE2 C:GLU592 4.1 27.7 1.0
OG1 C:THR633 4.2 25.2 1.0
CD2 C:HIS563 4.2 22.0 1.0
O C:HIS563 4.3 24.5 1.0
CD2 C:HIS567 4.3 26.4 1.0
O C:HOH991 4.3 30.2 1.0
CD2 C:HIS595 4.4 25.1 1.0
CB C:ASP564 4.4 23.3 1.0
O C:HOH1048 4.4 43.0 1.0
OD2 C:ASP674 4.4 28.2 1.0
O C:THR633 4.5 25.6 1.0
NE2 C:HIS567 4.5 24.6 1.0
NE2 C:HIS563 4.5 22.8 1.0
CD2 C:HIS525 4.6 28.4 1.0
NE2 C:HIS525 4.6 30.2 1.0
CB C:THR633 4.6 25.9 1.0
CA C:ASP564 4.8 23.3 1.0
CG C:GLU592 4.9 25.4 1.0
CD C:GLU592 4.9 27.5 1.0

Magnesium binding site 4 out of 4 in 5se8

Go back to Magnesium Binding Sites List in 5se8
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(2-Methyl-5-Phenyl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide


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- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(2-Methyl-5-Phenyl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:31.8
occ:1.00
 O D:HOH960 2.0 24.6 1.0
O D:HOH928 2.0 28.9 1.0
O D:HOH918 2.1 25.0 1.0
O D:HOH954 2.1 28.3 1.0
OD1 D:ASP564 2.1 29.1 1.0
O D:HOH975 2.1 27.9 1.0
CG D:ASP564 3.1 27.8 1.0
OD2 D:ASP564 3.5 35.3 1.0
ZN D:ZN801 3.7 33.9 1.0
O D:HOH949 3.9 41.4 1.0
OE2 D:GLU592 4.0 30.0 1.0
O D:HOH968 4.1 39.0 1.0
NE2 D:HIS595 4.1 32.8 1.0
OG1 D:THR633 4.2 30.9 1.0
CD2 D:HIS567 4.3 32.1 1.0
CD2 D:HIS563 4.4 30.1 1.0
OD2 D:ASP674 4.4 31.9 1.0
O D:HIS563 4.4 28.0 1.0
NE2 D:HIS525 4.5 35.1 1.0
O D:THR633 4.5 36.0 1.0
CD2 D:HIS595 4.5 32.7 1.0
CB D:ASP564 4.5 29.1 1.0
NE2 D:HIS567 4.5 30.3 1.0
CD2 D:HIS525 4.5 34.0 1.0
CB D:THR633 4.7 30.2 1.0
NE2 D:HIS563 4.8 25.9 1.0
CA D:ASP564 4.9 28.2 1.0
CD D:GLU592 4.9 35.2 1.0
CG D:GLU592 5.0 36.3 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 03:19:50 2024

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