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Magnesium in PDB 5sfl: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[5-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[5-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-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-[5-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-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-[5-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide, PDB code: 5sfl 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) 43.44 / 2.13
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.036, 135.036, 234.927, 90, 90, 120
R / Rfree (%) 18.7 / 22.7

Other elements in 5sfl:

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

Magnesium binding site 1 out of 4 in 5sfl

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

b:31.8
occ:1.00
 O A:HOH989 2.0 28.9 1.0
O A:HOH965 2.0 31.1 1.0
OD1 A:ASP564 2.0 31.9 1.0
O A:HOH941 2.1 28.1 1.0
O A:HOH951 2.1 26.8 1.0
O A:HOH927 2.2 30.6 1.0
CG A:ASP564 3.0 32.1 1.0
OD2 A:ASP564 3.4 35.2 1.0
ZN A:ZN801 3.7 37.5 1.0
NE2 A:HIS595 4.0 35.1 1.0
OE2 A:GLU592 4.0 37.1 1.0
O A:HOH976 4.0 49.5 1.0
CD2 A:HIS567 4.2 35.5 1.0
CD2 A:HIS595 4.2 32.8 1.0
CD2 A:HIS563 4.3 31.4 1.0
OG1 A:THR633 4.3 33.6 1.0
O A:HIS563 4.3 30.3 1.0
CB A:ASP564 4.3 31.3 1.0
NE2 A:HIS567 4.4 32.6 1.0
O A:HOH943 4.4 45.3 1.0
O A:THR633 4.5 30.9 1.0
OD2 A:ASP674 4.5 38.4 1.0
NE2 A:HIS563 4.6 33.4 1.0
CD2 A:HIS525 4.7 36.9 1.0
CA A:ASP564 4.7 31.6 1.0
NE2 A:HIS525 4.8 36.6 1.0
CB A:THR633 4.8 30.4 1.0
CD A:GLU592 4.9 37.5 1.0
CG A:GLU592 4.9 33.8 1.0

Magnesium binding site 2 out of 4 in 5sfl

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

b:29.5
occ:1.00
 O B:HOH932 1.9 28.6 1.0
O B:HOH952 2.0 28.9 1.0
OD1 B:ASP564 2.0 29.8 1.0
O B:HOH949 2.1 23.8 1.0
O B:HOH1000 2.1 27.1 1.0
O B:HOH922 2.1 26.4 1.0
CG B:ASP564 3.1 28.8 1.0
OD2 B:ASP564 3.4 32.6 1.0
ZN B:ZN801 3.7 35.8 1.0
OE2 B:GLU592 4.0 29.9 1.0
O B:HOH944 4.0 47.6 1.0
NE2 B:HIS595 4.0 33.8 1.0
O B:HOH1002 4.1 53.5 1.0
OG1 B:THR633 4.2 29.1 1.0
CD2 B:HIS563 4.2 28.7 1.0
CD2 B:HIS595 4.3 34.3 1.0
O B:HIS563 4.3 33.8 1.0
CD2 B:HIS567 4.3 30.9 1.0
OD2 B:ASP674 4.4 32.1 1.0
CB B:ASP564 4.4 28.6 1.0
NE2 B:HIS567 4.5 31.9 1.0
NE2 B:HIS563 4.5 28.3 1.0
O B:THR633 4.6 33.0 1.0
CB B:THR633 4.6 31.1 1.0
O B:HOH960 4.7 39.6 1.0
CD2 B:HIS525 4.7 30.9 1.0
CA B:ASP564 4.7 30.4 1.0
NE2 B:HIS525 4.8 32.8 1.0
CD B:GLU592 4.8 31.7 1.0
CG B:GLU592 4.8 32.7 1.0

Magnesium binding site 3 out of 4 in 5sfl

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

b:32.0
occ:1.00
 O C:HOH943 1.9 31.3 1.0
O C:HOH933 2.0 32.7 1.0
O C:HOH979 2.0 28.5 1.0
O C:HOH961 2.0 28.9 1.0
OD1 C:ASP564 2.0 31.8 1.0
O C:HOH945 2.2 28.4 1.0
CG C:ASP564 3.0 31.4 1.0
OD2 C:ASP564 3.4 32.0 1.0
ZN C:ZN801 3.7 39.2 1.0
NE2 C:HIS595 4.1 35.2 1.0
OE2 C:GLU592 4.1 36.0 1.0
CD2 C:HIS563 4.2 31.3 1.0
CD2 C:HIS567 4.2 36.5 1.0
OG1 C:THR633 4.3 35.1 1.0
OD2 C:ASP674 4.3 34.9 1.0
O C:HIS563 4.3 31.8 1.0
CD2 C:HIS595 4.4 33.9 1.0
CB C:ASP564 4.4 30.2 1.0
NE2 C:HIS567 4.4 36.9 1.0
NE2 C:HIS563 4.5 33.5 1.0
O C:THR633 4.6 37.0 1.0
CD2 C:HIS525 4.6 37.9 1.0
CB C:THR633 4.7 37.0 1.0
O C:HOH969 4.7 49.0 1.0
CA C:ASP564 4.8 31.4 1.0
NE2 C:HIS525 4.8 36.3 1.0
CG C:GLU592 4.9 33.8 1.0
CD C:GLU592 4.9 35.4 1.0

Magnesium binding site 4 out of 4 in 5sfl

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

b:40.8
occ:1.00
 O D:HOH910 2.0 29.4 1.0
O D:HOH958 2.0 42.4 1.0
O D:HOH937 2.1 37.9 1.0
O D:HOH920 2.1 38.3 1.0
OD1 D:ASP564 2.1 38.6 1.0
O D:HOH954 2.2 28.8 1.0
CG D:ASP564 3.1 38.8 1.0
OD2 D:ASP564 3.4 44.4 1.0
ZN D:ZN801 3.8 47.0 1.0
O D:HOH950 3.8 45.5 1.0
OE2 D:GLU592 4.0 42.4 1.0
O D:HOH955 4.2 45.9 1.0
CD2 D:HIS567 4.2 48.1 1.0
OD2 D:ASP674 4.3 41.2 1.0
NE2 D:HIS595 4.3 48.1 1.0
CD2 D:HIS563 4.3 36.1 1.0
OG1 D:THR633 4.3 43.6 1.0
NE2 D:HIS567 4.4 47.2 1.0
CB D:ASP564 4.5 37.1 1.0
O D:HIS563 4.5 39.3 1.0
CD2 D:HIS595 4.5 47.5 1.0
O D:THR633 4.6 43.6 1.0
CD2 D:HIS525 4.6 47.5 1.0
NE2 D:HIS563 4.7 36.3 1.0
NE2 D:HIS525 4.7 48.0 1.0
CB D:THR633 4.8 42.7 1.0
CA D:ASP564 4.9 35.7 1.0
CD D:GLU592 4.9 46.3 1.0
O D:HOH960 4.9 46.0 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 19:30:11 2025

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