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Magnesium in PDB 5sdv: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide, PDB code: 5sdv 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) 43.73 / 2.15
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.343, 135.343, 235.651, 90, 90, 120
R / Rfree (%) 17.5 / 23.2

Other elements in 5sdv:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide 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 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide (pdb code 5sdv). 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- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide, PDB code: 5sdv:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sdv

Go back to Magnesium Binding Sites List in 5sdv
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide


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- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:23.4
occ:1.00
 O A:HOH956 1.9 25.9 1.0
O A:HOH1020 2.0 23.0 1.0
OD1 A:ASP564 2.0 23.1 1.0
O A:HOH963 2.1 19.1 1.0
O A:HOH950 2.1 19.7 1.0
O A:HOH932 2.3 22.4 1.0
CG A:ASP564 3.0 24.8 1.0
OD2 A:ASP564 3.4 26.9 1.0
ZN A:ZN801 3.8 27.4 1.0
O A:HOH1019 3.8 46.9 1.0
O A:HOH994 3.9 27.8 1.0
NE2 A:HIS595 4.1 24.0 1.0
OE2 A:GLU592 4.1 27.3 1.0
CD2 A:HIS567 4.3 29.6 1.0
OG1 A:THR633 4.3 24.4 1.0
OD2 A:ASP674 4.3 38.8 1.0
O A:HOH987 4.4 34.6 1.0
CD2 A:HIS563 4.4 19.8 1.0
CD2 A:HIS595 4.4 22.4 1.0
CB A:ASP564 4.4 21.3 1.0
O A:HIS563 4.4 24.0 1.0
NE2 A:HIS567 4.5 25.2 1.0
O A:THR633 4.5 29.6 1.0
CD2 A:HIS525 4.6 29.2 1.0
NE2 A:HIS525 4.7 25.7 1.0
NE2 A:HIS563 4.7 22.1 1.0
CA A:ASP564 4.8 23.3 1.0
CG A:GLU592 4.8 26.3 1.0
CB A:THR633 4.9 26.8 1.0
CD A:GLU592 4.9 26.5 1.0

Magnesium binding site 2 out of 4 in 5sdv

Go back to Magnesium Binding Sites List in 5sdv
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide


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- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:22.7
occ:1.00
 O B:HOH946 1.8 16.6 1.0
O B:HOH931 1.9 17.5 1.0
O B:HOH923 2.0 17.7 1.0
O B:HOH1021 2.1 23.1 1.0
OD1 B:ASP564 2.1 22.1 1.0
O B:HOH947 2.2 16.4 1.0
CG B:ASP564 3.2 19.9 1.0
OD2 B:ASP564 3.5 20.5 1.0
ZN B:ZN801 3.8 25.3 1.0
OE2 B:GLU592 4.0 24.0 1.0
O B:HOH990 4.0 27.7 1.0
NE2 B:HIS595 4.1 23.8 1.0
OD2 B:ASP674 4.1 31.7 1.0
OG1 B:THR633 4.2 25.3 1.0
CD2 B:HIS563 4.2 22.1 1.0
CD2 B:HIS595 4.4 24.4 1.0
O B:HOH980 4.4 29.8 1.0
O B:THR633 4.4 21.9 1.0
O B:HIS563 4.5 23.1 1.0
CD2 B:HIS567 4.5 22.4 1.0
CB B:ASP564 4.5 19.7 1.0
CB B:THR633 4.6 23.8 1.0
NE2 B:HIS567 4.6 20.1 1.0
NE2 B:HIS563 4.6 18.3 1.0
CD2 B:HIS525 4.7 24.7 1.0
NE2 B:HIS525 4.7 24.9 1.0
CG B:GLU592 4.8 24.8 1.0
CD B:GLU592 4.8 26.2 1.0
CA B:ASP564 4.9 20.6 1.0

Magnesium binding site 3 out of 4 in 5sdv

Go back to Magnesium Binding Sites List in 5sdv
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide


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- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:22.7
occ:1.00
 O C:HOH986 2.0 21.4 1.0
O C:HOH999 2.0 22.1 1.0
O C:HOH947 2.0 24.6 1.0
O C:HOH1027 2.1 20.7 1.0
OD1 C:ASP564 2.1 23.1 1.0
O C:HOH925 2.2 20.8 1.0
CG C:ASP564 3.2 27.3 1.0
OD2 C:ASP564 3.5 27.2 1.0
ZN C:ZN801 3.8 30.2 1.0
O C:HOH987 4.0 30.6 1.0
OE2 C:GLU592 4.0 24.7 1.0
NE2 C:HIS595 4.1 24.6 1.0
CD2 C:HIS567 4.2 28.4 1.0
CD2 C:HIS563 4.2 21.6 1.0
O C:HIS563 4.3 24.9 1.0
OD2 C:ASP674 4.4 36.5 1.0
OG1 C:THR633 4.4 24.5 1.0
NE2 C:HIS567 4.4 29.0 1.0
O C:HOH1014 4.4 31.7 1.0
CD2 C:HIS595 4.5 24.1 1.0
CB C:ASP564 4.5 22.3 1.0
O C:THR633 4.5 28.2 1.0
NE2 C:HIS563 4.7 19.1 1.0
CB C:THR633 4.7 25.2 1.0
CD2 C:HIS525 4.7 32.1 1.0
NE2 C:HIS525 4.7 29.4 1.0
CG C:GLU592 4.7 24.0 1.0
CD C:GLU592 4.8 26.8 1.0
CA C:ASP564 4.9 23.1 1.0
OD1 C:ASP674 5.0 26.2 1.0

Magnesium binding site 4 out of 4 in 5sdv

Go back to Magnesium Binding Sites List in 5sdv
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide


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- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:32.8
occ:1.00
 O D:HOH965 2.0 27.1 1.0
O D:HOH935 2.1 31.1 1.0
O D:HOH981 2.1 32.7 1.0
O D:HOH922 2.1 22.3 1.0
OD1 D:ASP564 2.2 31.9 1.0
O D:HOH904 2.2 27.9 1.0
CG D:ASP564 3.2 28.8 1.0
OD2 D:ASP564 3.6 38.6 1.0
ZN D:ZN801 3.9 37.0 1.0
OE2 D:GLU592 3.9 32.0 1.0
NE2 D:HIS595 4.0 37.5 1.0
O D:HOH945 4.0 34.3 1.0
O D:HOH978 4.1 45.6 1.0
CD2 D:HIS567 4.2 37.3 1.0
OG1 D:THR633 4.3 31.4 1.0
CD2 D:HIS595 4.3 36.6 1.0
NE2 D:HIS567 4.4 33.7 1.0
O D:HIS563 4.4 31.6 1.0
CD2 D:HIS563 4.4 28.2 1.0
OD2 D:ASP674 4.4 33.8 1.0
CB D:ASP564 4.5 29.8 1.0
O D:THR633 4.6 35.5 1.0
CD2 D:HIS525 4.7 37.5 1.0
NE2 D:HIS525 4.7 39.3 1.0
CD D:GLU592 4.8 38.1 1.0
CA D:ASP564 4.8 27.5 1.0
CB D:THR633 4.9 33.8 1.0
CG D:GLU592 4.9 39.1 1.0
NE2 D:HIS563 4.9 23.5 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 03:14:31 2024

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