Magnesium in PDB 5sfv: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-(1-Cyclopentylpyrazol-3-Yl)-2- Methylpyrazole-3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-(1-Cyclopentylpyrazol-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-Cyclopentylpyrazol-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-Cyclopentylpyrazol-3-Yl)-2- Methylpyrazole-3-Carboxamide, PDB code: 5sfv 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) 43.58 / 2.41
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.925, 134.925, 234.826, 90, 90, 120
R / Rfree (%) 18.5 / 24.9

Other elements in 5sfv:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-(1-Cyclopentylpyrazol-3-Yl)-2- Methylpyrazole-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)-N-(1-Cyclopentylpyrazol-3-Yl)-2- Methylpyrazole-3-Carboxamide (pdb code 5sfv). 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-Cyclopentylpyrazol-3-Yl)-2- Methylpyrazole-3-Carboxamide, PDB code: 5sfv:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sfv

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

b:20.7
occ:1.00
 O A:HOH909 2.0 19.1 1.0
OD1 A:ASP564 2.0 23.3 1.0
O A:HOH930 2.0 15.0 1.0
O A:HOH980 2.1 18.8 1.0
O A:HOH954 2.2 26.2 1.0
O A:HOH939 2.2 19.9 1.0
CG A:ASP564 2.9 21.7 1.0
OD2 A:ASP564 3.2 21.2 1.0
O A:HOH966 3.7 29.3 1.0
ZN A:ZN801 3.8 25.1 1.0
NE2 A:HIS595 4.0 22.8 1.0
O A:HOH982 4.0 27.6 1.0
CD2 A:HIS567 4.0 28.2 1.0
OE2 A:GLU592 4.3 25.7 1.0
NE2 A:HIS567 4.3 28.6 1.0
CB A:ASP564 4.3 20.2 1.0
CD2 A:HIS563 4.3 18.2 1.0
O A:HOH997 4.3 35.8 1.0
CD2 A:HIS595 4.4 22.9 1.0
O A:HIS563 4.4 23.5 1.0
OG1 A:THR633 4.5 25.3 1.0
CD2 A:HIS525 4.5 26.1 1.0
NE2 A:HIS525 4.5 25.7 1.0
OD2 A:ASP674 4.6 27.0 1.0
NE2 A:HIS563 4.6 17.2 1.0
CA A:ASP564 4.7 21.4 1.0
O A:THR633 4.7 22.8 1.0
CG A:GLU592 4.9 24.6 1.0
CB A:THR633 4.9 22.0 1.0
O A:HOH998 5.0 32.3 1.0

Magnesium binding site 2 out of 4 in 5sfv

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

b:12.8
occ:1.00
 O B:HOH907 1.9 9.5 1.0
O B:HOH927 1.9 10.2 1.0
O B:HOH921 2.0 12.8 1.0
O B:HOH989 2.1 12.7 1.0
O B:HOH930 2.2 10.6 1.0
OD1 B:ASP564 2.2 20.5 1.0
CG B:ASP564 3.3 20.6 1.0
OE2 B:GLU592 3.6 20.8 1.0
OD2 B:ASP564 3.6 19.5 1.0
O B:HOH1016 3.9 42.4 1.0
O B:HOH956 4.0 22.4 1.0
NE2 B:HIS595 4.0 22.6 1.0
OG1 B:THR633 4.1 19.3 1.0
ZN B:ZN801 4.1 26.1 1.0
O B:HIS563 4.2 21.8 1.0
CD2 B:HIS595 4.3 22.2 1.0
CD2 B:HIS567 4.3 19.0 1.0
CD2 B:HIS563 4.3 15.5 1.0
OD2 B:ASP674 4.4 29.5 1.0
NE2 B:HIS567 4.4 19.5 1.0
O B:THR633 4.4 18.8 1.0
CD B:GLU592 4.5 22.7 1.0
CG B:GLU592 4.5 22.7 1.0
O B:HOH959 4.5 32.6 1.0
CB B:THR633 4.6 19.3 1.0
CB B:ASP564 4.6 21.5 1.0
NE2 B:HIS563 4.7 16.1 1.0
NE2 B:HIS525 4.8 20.0 1.0
CD2 B:HIS525 4.9 22.7 1.0
CA B:ASP564 4.9 20.5 1.0
O B:HOH997 5.0 27.1 1.0
C B:THR633 5.0 17.9 1.0

Magnesium binding site 3 out of 4 in 5sfv

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

b:22.4
occ:1.00
 O C:HOH996 1.9 20.1 1.0
OD1 C:ASP564 2.1 25.6 1.0
O C:HOH921 2.1 22.3 1.0
O C:HOH942 2.1 21.0 1.0
O C:HOH946 2.2 20.4 1.0
O C:HOH960 2.2 16.9 1.0
CG C:ASP564 3.1 24.7 1.0
OD2 C:ASP564 3.5 27.2 1.0
ZN C:ZN801 3.9 31.2 1.0
NE2 C:HIS595 3.9 26.7 1.0
CD2 C:HIS567 4.1 26.4 1.0
OE2 C:GLU592 4.1 24.5 1.0
CD2 C:HIS563 4.2 17.8 1.0
NE2 C:HIS567 4.2 27.9 1.0
O C:HIS563 4.3 22.8 1.0
CD2 C:HIS595 4.4 27.2 1.0
O C:HOH958 4.4 32.8 1.0
OG1 C:THR633 4.4 26.6 1.0
CB C:ASP564 4.5 23.7 1.0
NE2 C:HIS563 4.5 16.0 1.0
OD2 C:ASP674 4.5 27.9 1.0
O C:THR633 4.6 28.5 1.0
CD2 C:HIS525 4.6 32.9 1.0
NE2 C:HIS525 4.7 35.0 1.0
CB C:THR633 4.8 27.0 1.0
CA C:ASP564 4.8 22.5 1.0
CG C:GLU592 4.9 23.8 1.0
CD C:GLU592 5.0 24.8 1.0
CE1 C:HIS595 5.0 28.8 1.0
O C:HOH1014 5.0 49.0 1.0

Magnesium binding site 4 out of 4 in 5sfv

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

b:25.9
occ:1.00
 O D:HOH956 2.0 33.8 1.0
OD1 D:ASP564 2.1 30.8 1.0
O D:HOH923 2.1 24.0 1.0
O D:HOH924 2.1 21.4 1.0
O D:HOH943 2.2 18.9 1.0
O D:HOH907 2.2 26.8 1.0
CG D:ASP564 3.0 30.8 1.0
OD2 D:ASP564 3.1 32.3 1.0
ZN D:ZN801 3.6 36.5 1.0
O D:HOH939 3.8 27.8 1.0
CD2 D:HIS563 4.2 27.1 1.0
O D:HOH951 4.2 39.7 1.0
OE2 D:GLU592 4.2 33.0 1.0
OG1 D:THR633 4.3 32.5 1.0
NE2 D:HIS595 4.3 32.6 1.0
CD2 D:HIS567 4.3 33.3 1.0
CB D:ASP564 4.4 29.8 1.0
O D:HIS563 4.4 27.6 1.0
CD2 D:HIS525 4.4 34.1 1.0
NE2 D:HIS567 4.4 35.5 1.0
NE2 D:HIS525 4.4 31.3 1.0
O D:THR633 4.4 35.1 1.0
OD2 D:ASP674 4.4 34.2 1.0
NE2 D:HIS563 4.5 27.2 1.0
CD2 D:HIS595 4.7 32.6 1.0
CA D:ASP564 4.8 32.4 1.0
CB D:THR633 4.8 32.1 1.0
OD1 D:ASP674 4.9 34.1 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 03:40:50 2024

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