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Magnesium in PDB 5seg: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide, PDB code: 5seg was solved by C.Joseph, K.Bleicher, 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) 43.71 / 2.29
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.29, 135.29, 235.561, 90, 90, 120
R / Rfree (%) 17.4 / 23.1

Other elements in 5seg:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide also contains other interesting chemical elements:

Bromine (Br) 4 atoms
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-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide (pdb code 5seg). 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-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide, PDB code: 5seg:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5seg

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-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-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:35.6
occ:1.00
 O A:HOH968 1.9 32.1 1.0
O A:HOH930 2.0 34.5 1.0
OD1 A:ASP564 2.0 34.9 1.0
O A:HOH919 2.1 26.6 1.0
O A:HOH926 2.1 36.0 1.0
O A:HOH940 2.1 34.2 1.0
CG A:ASP564 3.0 35.5 1.0
OD2 A:ASP564 3.2 36.7 1.0
ZN A:ZN801 3.7 41.7 1.0
O A:HOH946 3.8 41.9 1.0
OE2 A:GLU592 4.1 39.4 1.0
NE2 A:HIS595 4.2 38.2 1.0
CD2 A:HIS563 4.3 34.0 1.0
O A:HOH942 4.3 50.4 1.0
OG1 A:THR633 4.3 40.3 1.0
CD2 A:HIS567 4.4 38.0 1.0
CB A:ASP564 4.4 34.9 1.0
OD2 A:ASP674 4.4 53.3 1.0
O A:THR633 4.4 44.0 1.0
O A:HIS563 4.5 35.0 1.0
NE2 A:HIS567 4.5 37.5 1.0
CD2 A:HIS595 4.6 36.4 1.0
NE2 A:HIS563 4.6 33.0 1.0
CD2 A:HIS525 4.6 45.7 1.0
NE2 A:HIS525 4.6 43.4 1.0
CB A:THR633 4.7 36.5 1.0
CA A:ASP564 4.8 39.6 1.0
CD A:GLU592 5.0 48.6 1.0
CG A:GLU592 5.0 40.8 1.0

Magnesium binding site 2 out of 4 in 5seg

Go back to Magnesium Binding Sites List in 5seg
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-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-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:30.6
occ:1.00
 O B:HOH969 2.0 32.7 1.0
OD1 B:ASP564 2.0 36.9 1.0
O B:HOH935 2.0 27.4 1.0
O B:HOH925 2.0 33.3 1.0
O B:HOH910 2.1 30.7 1.0
O B:HOH947 2.1 29.3 1.0
CG B:ASP564 3.0 31.7 1.0
OD2 B:ASP564 3.3 37.8 1.0
O B:HOH961 3.7 41.7 1.0
ZN B:ZN801 3.8 41.9 1.0
OE2 B:GLU592 4.0 41.9 1.0
NE2 B:HIS595 4.2 40.0 1.0
CD2 B:HIS563 4.2 31.4 1.0
CD2 B:HIS567 4.3 36.0 1.0
O B:HOH950 4.3 43.5 1.0
OG1 B:THR633 4.3 32.5 1.0
CB B:ASP564 4.4 30.4 1.0
O B:HIS563 4.4 36.9 1.0
OD2 B:ASP674 4.4 39.1 1.0
CD2 B:HIS595 4.4 38.2 1.0
NE2 B:HIS567 4.4 34.5 1.0
NE2 B:HIS563 4.5 34.9 1.0
O B:THR633 4.6 34.2 1.0
CD2 B:HIS525 4.6 42.4 1.0
NE2 B:HIS525 4.7 41.7 1.0
CA B:ASP564 4.7 33.0 1.0
CB B:THR633 4.7 36.6 1.0
CD B:GLU592 4.8 41.0 1.0
CG B:GLU592 4.9 36.1 1.0

Magnesium binding site 3 out of 4 in 5seg

Go back to Magnesium Binding Sites List in 5seg
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-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-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:36.2
occ:1.00
 O C:HOH927 1.9 36.0 1.0
O C:HOH946 1.9 35.4 1.0
O C:HOH935 2.0 36.1 1.0
OD1 C:ASP564 2.1 34.9 1.0
O C:HOH968 2.2 33.7 1.0
O C:HOH945 2.2 33.2 1.0
CG C:ASP564 3.1 36.2 1.0
OD2 C:ASP564 3.4 36.5 1.0
ZN C:ZN801 3.8 41.8 1.0
O C:HOH954 3.9 47.7 1.0
NE2 C:HIS595 4.1 43.2 1.0
OE2 C:GLU592 4.2 46.1 1.0
CD2 C:HIS567 4.2 38.0 1.0
CD2 C:HIS563 4.3 34.2 1.0
O C:HIS563 4.3 41.5 1.0
NE2 C:HIS567 4.3 39.0 1.0
OG1 C:THR633 4.3 36.9 1.0
CD2 C:HIS595 4.4 41.7 1.0
OD2 C:ASP674 4.4 42.3 1.0
O C:HOH962 4.4 44.9 1.0
O C:HOH975 4.5 63.6 1.0
CB C:ASP564 4.5 31.4 1.0
O C:THR633 4.6 39.6 1.0
NE2 C:HIS563 4.7 36.5 1.0
CD2 C:HIS525 4.7 43.7 1.0
CB C:THR633 4.7 42.6 1.0
NE2 C:HIS525 4.8 43.2 1.0
CA C:ASP564 4.8 31.5 1.0
CG C:GLU592 4.9 39.5 1.0
CD C:GLU592 4.9 44.1 1.0

Magnesium binding site 4 out of 4 in 5seg

Go back to Magnesium Binding Sites List in 5seg
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-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-[(5- Bromo-1-Methyl-2-Oxopyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:48.9
occ:1.00
 O D:HOH921 1.9 45.6 1.0
O D:HOH919 2.1 40.9 1.0
O D:HOH901 2.1 44.1 1.0
O D:HOH911 2.1 44.5 1.0
OD1 D:ASP564 2.2 49.8 1.0
O D:HOH903 2.3 38.1 1.0
CG D:ASP564 3.1 40.9 1.0
OD2 D:ASP564 3.4 52.5 1.0
O D:HOH918 3.8 48.3 1.0
O D:HOH917 3.9 43.9 1.0
ZN D:ZN801 3.9 52.5 1.0
OE2 D:GLU592 3.9 49.7 1.0
NE2 D:HIS595 4.1 49.9 1.0
CD2 D:HIS567 4.2 60.3 1.0
OG1 D:THR633 4.3 47.5 1.0
NE2 D:HIS567 4.3 53.2 1.0
CD2 D:HIS563 4.4 41.2 1.0
CD2 D:HIS595 4.5 52.7 1.0
CB D:ASP564 4.5 45.2 1.0
O D:THR633 4.5 50.8 1.0
OD2 D:ASP674 4.5 51.5 1.0
O D:HIS563 4.5 44.6 1.0
CD2 D:HIS525 4.6 60.9 1.0
NE2 D:HIS525 4.7 62.0 1.0
NE2 D:HIS563 4.7 39.0 1.0
CD D:GLU592 4.8 48.8 1.0
CA D:ASP564 4.8 45.0 1.0
CB D:THR633 4.8 50.4 1.0
CG D:GLU592 5.0 51.1 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: Tue Aug 12 19:19:19 2025

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