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Magnesium in PDB 5sfq: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-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)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide, PDB code: 5sfq was solved by C.Joseph, J.U.Peters, 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) 43.26 / 2.21
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.458, 134.458, 234.587, 90, 90, 120
R / Rfree (%) 18.6 / 24.8

Other elements in 5sfq:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Fluorine (F) 8 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)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide (pdb code 5sfq). 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)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide, PDB code: 5sfq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sfq

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-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)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:22.2
occ:1.00
 O A:HOH1002 2.0 18.6 1.0
OD1 A:ASP564 2.0 23.5 1.0
O A:HOH956 2.0 22.2 1.0
O A:HOH952 2.1 18.4 1.0
O A:HOH926 2.1 18.3 1.0
O A:HOH960 2.3 27.7 1.0
CG A:ASP564 3.0 22.5 1.0
OD2 A:ASP564 3.4 24.3 1.0
ZN A:ZN801 3.8 28.0 1.0
O A:HOH989 3.8 20.8 1.0
NE2 A:HIS595 3.9 28.0 1.0
CD2 A:HIS567 4.2 28.3 1.0
OE2 A:GLU592 4.2 28.0 1.0
O A:HOH998 4.2 32.1 1.0
NE2 A:HIS567 4.3 26.6 1.0
CD2 A:HIS595 4.3 24.4 1.0
CD2 A:HIS563 4.3 20.8 1.0
O A:HOH1027 4.3 41.0 1.0
OG1 A:THR633 4.3 26.7 1.0
CB A:ASP564 4.4 20.1 1.0
O A:HIS563 4.4 21.0 1.0
OD2 A:ASP674 4.5 36.0 1.0
NE2 A:HIS525 4.5 24.4 1.0
CD2 A:HIS525 4.6 28.0 1.0
O A:THR633 4.6 27.2 1.0
NE2 A:HIS563 4.6 19.5 1.0
CB A:THR633 4.7 23.5 1.0
CA A:ASP564 4.7 21.3 1.0
CG A:GLU592 4.9 26.4 1.0
CD A:GLU592 5.0 28.5 1.0

Magnesium binding site 2 out of 4 in 5sfq

Go back to Magnesium Binding Sites List in 5sfq
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-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)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:21.4
occ:1.00
 O B:HOH939 1.9 21.0 1.0
O B:HOH931 2.0 12.7 1.0
O B:HOH917 2.1 15.1 1.0
OD1 B:ASP564 2.1 21.6 1.0
O B:HOH992 2.1 13.0 1.0
O B:HOH974 2.2 17.2 1.0
CG B:ASP564 3.2 22.5 1.0
OD2 B:ASP564 3.5 20.6 1.0
ZN B:ZN801 3.8 26.0 1.0
OE2 B:GLU592 3.9 22.7 1.0
O B:HOH956 4.0 27.5 1.0
OG1 B:THR633 4.1 18.6 1.0
NE2 B:HIS595 4.1 25.1 1.0
CD2 B:HIS563 4.1 18.3 1.0
O B:HOH1043 4.2 49.2 1.0
OD2 B:ASP674 4.2 22.9 1.0
CD2 B:HIS567 4.3 23.4 1.0
NE2 B:HIS567 4.4 21.0 1.0
CD2 B:HIS595 4.4 25.4 1.0
O B:HIS563 4.4 24.5 1.0
O B:HOH978 4.4 34.7 1.0
O B:THR633 4.5 18.3 1.0
CB B:ASP564 4.5 21.9 1.0
NE2 B:HIS563 4.5 17.3 1.0
CB B:THR633 4.5 20.6 1.0
NE2 B:HIS525 4.6 23.6 1.0
CD2 B:HIS525 4.6 24.3 1.0
CG B:GLU592 4.7 23.5 1.0
CD B:GLU592 4.7 23.3 1.0
CA B:ASP564 4.9 22.2 1.0

Magnesium binding site 3 out of 4 in 5sfq

Go back to Magnesium Binding Sites List in 5sfq
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-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)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:27.2
occ:1.00
 O C:HOH932 2.0 24.4 1.0
O C:HOH923 2.0 24.1 1.0
O C:HOH996 2.0 21.4 1.0
O C:HOH922 2.1 21.7 1.0
OD1 C:ASP564 2.1 25.0 1.0
O C:HOH979 2.2 25.2 1.0
CG C:ASP564 3.2 23.6 1.0
OD2 C:ASP564 3.6 21.3 1.0
O C:HOH987 3.8 34.2 1.0
ZN C:ZN801 3.9 31.9 1.0
CD2 C:HIS567 4.0 26.1 1.0
NE2 C:HIS595 4.0 28.6 1.0
NE2 C:HIS567 4.1 31.0 1.0
O C:HOH969 4.1 37.0 1.0
OE2 C:GLU592 4.2 29.9 1.0
CD2 C:HIS563 4.2 22.6 1.0
O C:HIS563 4.3 21.2 1.0
CD2 C:HIS595 4.4 28.2 1.0
OD2 C:ASP674 4.4 29.3 1.0
NE2 C:HIS525 4.4 33.8 1.0
CD2 C:HIS525 4.5 33.6 1.0
NE2 C:HIS563 4.5 21.5 1.0
OG1 C:THR633 4.5 26.4 1.0
CB C:ASP564 4.5 22.2 1.0
O C:HOH1029 4.5 44.2 1.0
O C:THR633 4.7 26.7 1.0
CA C:ASP564 4.8 22.1 1.0
CB C:THR633 4.9 27.8 1.0
CG C:GLU592 4.9 27.2 1.0
CD C:GLU592 5.0 29.9 1.0

Magnesium binding site 4 out of 4 in 5sfq

Go back to Magnesium Binding Sites List in 5sfq
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-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)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:26.5
occ:1.00
 O D:HOH977 2.0 21.6 1.0
O D:HOH935 2.1 21.0 1.0
OD1 D:ASP564 2.1 28.4 1.0
O D:HOH929 2.1 25.8 1.0
O D:HOH960 2.2 24.0 1.0
O D:HOH932 2.2 21.8 1.0
CG D:ASP564 3.1 26.6 1.0
OD2 D:ASP564 3.5 30.0 1.0
ZN D:ZN801 3.8 32.0 1.0
O D:HOH975 3.9 33.9 1.0
O D:HOH988 3.9 25.1 1.0
NE2 D:HIS567 4.0 32.3 1.0
CD2 D:HIS567 4.1 40.9 1.0
OE2 D:GLU592 4.1 28.8 1.0
NE2 D:HIS595 4.2 29.3 1.0
CD2 D:HIS525 4.3 32.3 1.0
NE2 D:HIS525 4.4 33.5 1.0
OG1 D:THR633 4.4 25.6 1.0
CD2 D:HIS563 4.4 23.9 1.0
CB D:ASP564 4.5 24.2 1.0
OD2 D:ASP674 4.5 27.7 1.0
O D:THR633 4.6 34.0 1.0
CD2 D:HIS595 4.6 33.3 1.0
O D:HIS563 4.7 24.5 1.0
NE2 D:HIS563 4.8 25.6 1.0
CA D:ASP564 4.8 22.9 1.0
CB D:THR633 4.9 29.6 1.0
CD D:GLU592 4.9 28.9 1.0
CG D:GLU592 4.9 31.3 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 03:38:48 2024

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