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Magnesium in PDB 5se5: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide, PDB code: 5se5 was solved by C.Joseph, K.Groebke-Zbinden, 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) 43.40 / 2.08
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.91, 134.91, 234.914, 90, 90, 120
R / Rfree (%) 18.6 / 22.6

Other elements in 5se5:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-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 6- Cyclopropyl-N-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide (pdb code 5se5). 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 6- Cyclopropyl-N-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide, PDB code: 5se5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5se5

Go back to Magnesium Binding Sites List in 5se5
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-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 6- Cyclopropyl-N-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:28.8
occ:1.00
 O A:HOH1007 1.9 29.5 1.0
O A:HOH951 1.9 30.4 1.0
O A:HOH922 2.0 25.4 1.0
OD1 A:ASP564 2.0 27.4 1.0
O A:HOH969 2.1 24.7 1.0
O A:HOH934 2.2 27.3 1.0
CG A:ASP564 3.1 29.4 1.0
OD2 A:ASP564 3.5 32.1 1.0
ZN A:ZN801 3.8 33.1 1.0
O A:HOH995 3.9 42.2 1.0
OE2 A:GLU592 4.0 34.2 1.0
NE2 A:HIS595 4.1 31.5 1.0
CD2 A:HIS567 4.2 36.2 1.0
OG1 A:THR633 4.3 30.3 1.0
CD2 A:HIS563 4.3 27.6 1.0
CD2 A:HIS595 4.3 31.0 1.0
O A:HIS563 4.4 28.1 1.0
NE2 A:HIS567 4.4 31.6 1.0
O A:HOH1012 4.4 58.0 1.0
CB A:ASP564 4.4 26.6 1.0
O A:HOH980 4.4 43.1 1.0
OD2 A:ASP674 4.4 35.0 1.0
O A:THR633 4.5 31.2 1.0
CD2 A:HIS525 4.6 31.7 1.0
NE2 A:HIS563 4.6 28.0 1.0
NE2 A:HIS525 4.7 30.7 1.0
CB A:THR633 4.8 29.5 1.0
CA A:ASP564 4.8 27.6 1.0
CG A:GLU592 4.8 31.0 1.0
CD A:GLU592 4.9 32.2 1.0

Magnesium binding site 2 out of 4 in 5se5

Go back to Magnesium Binding Sites List in 5se5
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-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 6- Cyclopropyl-N-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:26.4
occ:1.00
 O B:HOH936 1.9 25.3 1.0
O B:HOH946 2.0 23.1 1.0
O B:HOH954 2.0 23.4 1.0
O B:HOH1002 2.1 26.2 1.0
OD1 B:ASP564 2.1 27.6 1.0
O B:HOH955 2.1 23.3 1.0
CG B:ASP564 3.1 27.3 1.0
OD2 B:ASP564 3.5 28.3 1.0
ZN B:ZN801 3.8 32.8 1.0
O B:HOH961 4.0 43.9 1.0
OE2 B:GLU592 4.0 29.6 1.0
NE2 B:HIS595 4.0 30.2 1.0
O B:HOH1014 4.1 53.5 1.0
CD2 B:HIS563 4.2 25.8 1.0
OG1 B:THR633 4.2 27.8 1.0
CD2 B:HIS567 4.3 26.9 1.0
CD2 B:HIS595 4.3 29.6 1.0
OD2 B:ASP674 4.3 30.8 1.0
NE2 B:HIS567 4.4 25.7 1.0
O B:HIS563 4.4 28.4 1.0
O B:HOH986 4.4 39.0 1.0
CB B:ASP564 4.5 28.0 1.0
NE2 B:HIS563 4.5 24.2 1.0
O B:THR633 4.5 26.8 1.0
CD2 B:HIS525 4.6 29.5 1.0
CB B:THR633 4.7 27.1 1.0
NE2 B:HIS525 4.7 29.0 1.0
CA B:ASP564 4.8 27.6 1.0
CD B:GLU592 4.8 29.3 1.0
CG B:GLU592 4.8 27.9 1.0

Magnesium binding site 3 out of 4 in 5se5

Go back to Magnesium Binding Sites List in 5se5
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-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 6- Cyclopropyl-N-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:31.1
occ:1.00
 O C:HOH959 1.9 30.4 1.0
O C:HOH932 2.0 29.8 1.0
O C:HOH985 2.1 31.8 1.0
OD1 C:ASP564 2.1 33.4 1.0
O C:HOH994 2.1 29.7 1.0
O C:HOH930 2.2 30.1 1.0
CG C:ASP564 3.1 30.5 1.0
OD2 C:ASP564 3.4 32.4 1.0
ZN C:ZN801 3.7 37.7 1.0
O C:HOH973 4.0 48.4 1.0
OE2 C:GLU592 4.1 35.6 1.0
CD2 C:HIS567 4.1 36.5 1.0
NE2 C:HIS595 4.2 34.8 1.0
CD2 C:HIS563 4.2 28.1 1.0
O C:HIS563 4.3 32.3 1.0
NE2 C:HIS567 4.3 36.8 1.0
OD2 C:ASP674 4.3 35.4 1.0
CB C:ASP564 4.4 29.9 1.0
OG1 C:THR633 4.4 35.0 1.0
CD2 C:HIS595 4.4 32.9 1.0
NE2 C:HIS563 4.5 27.5 1.0
O C:HOH983 4.5 44.0 1.0
CD2 C:HIS525 4.5 38.8 1.0
O C:THR633 4.6 32.6 1.0
NE2 C:HIS525 4.6 38.0 1.0
CB C:THR633 4.7 33.5 1.0
CA C:ASP564 4.8 29.9 1.0
CG C:GLU592 4.9 31.2 1.0
CD C:GLU592 4.9 33.1 1.0

Magnesium binding site 4 out of 4 in 5se5

Go back to Magnesium Binding Sites List in 5se5
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-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 6- Cyclopropyl-N-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:36.0
occ:1.00
 O D:HOH973 2.1 27.5 1.0
O D:HOH979 2.1 37.1 1.0
O D:HOH923 2.1 33.4 1.0
O D:HOH920 2.1 29.1 1.0
OD1 D:ASP564 2.1 33.2 1.0
O D:HOH940 2.2 32.6 1.0
CG D:ASP564 3.1 35.4 1.0
OD2 D:ASP564 3.5 41.1 1.0
ZN D:ZN801 3.8 42.4 1.0
OE2 D:GLU592 4.0 40.3 1.0
O D:HOH957 4.0 39.0 1.0
O D:HOH968 4.1 49.0 1.0
NE2 D:HIS595 4.1 43.5 1.0
CD2 D:HIS567 4.2 48.2 1.0
OG1 D:THR633 4.2 38.0 1.0
NE2 D:HIS567 4.3 46.7 1.0
CD2 D:HIS563 4.4 33.5 1.0
O D:HIS563 4.4 35.6 1.0
CD2 D:HIS595 4.4 42.1 1.0
OD2 D:ASP674 4.4 40.4 1.0
CB D:ASP564 4.5 34.9 1.0
CD2 D:HIS525 4.6 44.5 1.0
O D:THR633 4.6 42.2 1.0
NE2 D:HIS525 4.7 44.6 1.0
NE2 D:HIS563 4.7 32.0 1.0
CB D:THR633 4.8 38.7 1.0
CA D:ASP564 4.8 34.4 1.0
CD D:GLU592 4.8 39.9 1.0
CG D:GLU592 4.9 39.7 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: Tue Aug 12 19:16:11 2025

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