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Magnesium in PDB 5sey: Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol, PDB code: 5sey 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) 43.70 / 2.29
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.139, 135.139, 235.509, 90, 90, 120
R / Rfree (%) 17.3 / 23.4

Other elements in 5sey:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol 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- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol (pdb code 5sey). 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- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol, PDB code: 5sey:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sey

Go back to Magnesium Binding Sites List in 5sey
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol


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- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:34.3
occ:1.00
 OD1 A:ASP564 2.0 29.1 1.0
O A:HOH961 2.0 29.5 1.0
O A:HOH944 2.0 28.2 1.0
O A:HOH917 2.0 33.6 1.0
O A:HOH916 2.0 28.7 1.0
O A:HOH904 2.1 27.9 1.0
CG A:ASP564 3.0 32.5 1.0
OD2 A:ASP564 3.4 35.3 1.0
ZN A:ZN801 3.8 40.8 1.0
OE2 A:GLU592 3.9 43.5 1.0
O A:HOH945 4.0 36.0 1.0
NE2 A:HIS595 4.0 34.7 1.0
O A:HOH925 4.1 45.4 1.0
CD2 A:HIS567 4.2 37.1 1.0
CD2 A:HIS595 4.3 34.6 1.0
CD2 A:HIS563 4.3 35.5 1.0
O A:HIS563 4.3 34.9 1.0
CB A:ASP564 4.4 31.8 1.0
NE2 A:HIS567 4.4 36.9 1.0
OG1 A:THR633 4.5 39.1 1.0
CD2 A:HIS525 4.6 36.7 1.0
O A:THR633 4.6 33.6 1.0
NE2 A:HIS525 4.6 38.7 1.0
OD2 A:ASP674 4.7 38.9 1.0
NE2 A:HIS563 4.7 32.1 1.0
CD A:GLU592 4.7 38.4 1.0
CA A:ASP564 4.8 34.8 1.0
CB A:THR633 4.8 37.1 1.0
CG A:GLU592 4.8 35.9 1.0
CE1 A:HIS595 5.0 32.2 1.0

Magnesium binding site 2 out of 4 in 5sey

Go back to Magnesium Binding Sites List in 5sey
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol


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- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:33.4
occ:1.00
 O B:HOH941 1.8 28.3 1.0
O B:HOH960 2.0 26.5 1.0
O B:HOH936 2.0 31.2 1.0
O B:HOH930 2.0 31.9 1.0
O B:HOH909 2.1 28.2 1.0
OD1 B:ASP564 2.1 29.4 1.0
CG B:ASP564 3.1 30.2 1.0
OD2 B:ASP564 3.4 34.2 1.0
O B:HOH979 3.7 55.5 1.0
ZN B:ZN801 3.8 40.0 1.0
OE2 B:GLU592 3.9 34.9 1.0
O B:HOH969 4.0 40.1 1.0
NE2 B:HIS595 4.1 36.3 1.0
OG1 B:THR633 4.1 37.2 1.0
O B:HOH962 4.2 43.3 1.0
CD2 B:HIS563 4.3 35.2 1.0
CD2 B:HIS567 4.3 32.8 1.0
CD2 B:HIS595 4.4 43.1 1.0
NE2 B:HIS567 4.4 37.4 1.0
O B:HIS563 4.4 34.8 1.0
OD2 B:ASP674 4.4 37.3 1.0
CD2 B:HIS525 4.5 42.1 1.0
O B:THR633 4.5 34.4 1.0
CB B:ASP564 4.5 31.6 1.0
NE2 B:HIS563 4.6 34.6 1.0
NE2 B:HIS525 4.6 43.0 1.0
CB B:THR633 4.7 34.0 1.0
CD B:GLU592 4.8 32.5 1.0
CG B:GLU592 4.8 29.9 1.0
CA B:ASP564 4.9 33.5 1.0
O B:HOH968 4.9 38.3 1.0

Magnesium binding site 3 out of 4 in 5sey

Go back to Magnesium Binding Sites List in 5sey
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol


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- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:34.9
occ:1.00
 OD1 C:ASP564 1.9 35.9 1.0
O C:HOH940 2.0 30.7 1.0
O C:HOH927 2.0 33.7 1.0
O C:HOH925 2.1 27.4 1.0
O C:HOH933 2.2 34.7 1.0
O C:HOH968 2.2 33.9 1.0
CG C:ASP564 2.9 34.9 1.0
OD2 C:ASP564 3.3 39.0 1.0
ZN C:ZN801 3.7 41.0 1.0
O C:HOH944 3.9 44.7 1.0
NE2 C:HIS595 4.0 38.5 1.0
CD2 C:HIS567 4.2 31.2 1.0
OE2 C:GLU592 4.2 38.0 1.0
CD2 C:HIS563 4.2 29.8 1.0
O C:HOH973 4.2 42.5 1.0
O C:HIS563 4.3 36.3 1.0
CB C:ASP564 4.3 32.2 1.0
CD2 C:HIS595 4.3 40.0 1.0
OG1 C:THR633 4.3 34.3 1.0
O C:HOH912 4.3 37.6 1.0
NE2 C:HIS567 4.3 33.5 1.0
OD2 C:ASP674 4.5 36.6 1.0
NE2 C:HIS563 4.6 34.0 1.0
CD2 C:HIS525 4.6 37.6 1.0
O C:THR633 4.7 33.3 1.0
CA C:ASP564 4.7 32.7 1.0
CB C:THR633 4.7 37.1 1.0
NE2 C:HIS525 4.7 34.8 1.0
CG C:GLU592 4.8 38.8 1.0
CD C:GLU592 4.9 38.5 1.0

Magnesium binding site 4 out of 4 in 5sey

Go back to Magnesium Binding Sites List in 5sey
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol


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- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethynyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:52.9
occ:1.00
 O D:HOH919 1.9 34.1 1.0
O D:HOH920 2.0 48.1 1.0
O D:HOH916 2.1 49.3 1.0
OD1 D:ASP564 2.1 56.1 1.0
O D:HOH903 2.1 51.4 1.0
O D:HOH905 2.2 46.8 1.0
CG D:ASP564 3.0 53.6 1.0
OD2 D:ASP564 3.2 66.7 1.0
O D:HOH912 3.6 45.6 1.0
ZN D:ZN801 3.7 56.0 1.0
OE2 D:GLU592 4.0 52.7 1.0
O D:HOH922 4.1 48.6 1.0
NE2 D:HIS595 4.1 60.9 1.0
CD2 D:HIS567 4.2 46.7 1.0
CD2 D:HIS563 4.3 48.1 1.0
OG1 D:THR633 4.4 51.2 1.0
CB D:ASP564 4.4 49.4 1.0
O D:HIS563 4.4 51.6 1.0
CD2 D:HIS595 4.5 63.8 1.0
NE2 D:HIS567 4.5 52.1 1.0
CD2 D:HIS525 4.5 61.9 1.0
NE2 D:HIS525 4.6 61.5 1.0
OD2 D:ASP674 4.6 59.1 1.0
NE2 D:HIS563 4.6 45.6 1.0
O D:THR633 4.7 55.4 1.0
CB D:THR633 4.7 53.0 1.0
CA D:ASP564 4.8 46.2 1.0
CD D:GLU592 4.9 52.9 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 03:27:16 2024

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