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Magnesium in PDB 5sez: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-6-Ethyl-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl) Pyridine-4-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-6-Ethyl-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl) Pyridine-4-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-6-Ethyl-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl) Pyridine-4-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-6-Ethyl-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl) Pyridine-4-Carboxamide, PDB code: 5sez 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) 43.67 / 1.99
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.732, 135.732, 235.193, 90, 90, 120
R / Rfree (%) 17.6 / 21.8

Other elements in 5sez:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-6-Ethyl-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl) Pyridine-4-Carboxamide also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-6-Ethyl-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl) Pyridine-4-Carboxamide (pdb code 5sez). 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- Chloro-6-Ethyl-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl) Pyridine-4-Carboxamide, PDB code: 5sez:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sez

Go back to Magnesium Binding Sites List in 5sez
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-6-Ethyl-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl) Pyridine-4-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 2- Chloro-6-Ethyl-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl) Pyridine-4-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:23.9
occ:1.00
 O A:HOH1028 1.9 25.1 1.0
O A:HOH988 2.0 23.4 1.0
O A:HOH930 2.0 20.7 1.0
OD1 A:ASP564 2.0 21.1 1.0
O A:HOH969 2.1 22.8 1.0
O A:HOH937 2.2 21.6 1.0
CG A:ASP564 3.0 26.0 1.0
OD2 A:ASP564 3.3 24.9 1.0
ZN A:ZN801 3.7 30.2 1.0
O A:HOH989 3.9 38.4 1.0
O A:HOH1002 3.9 31.8 1.0
OE2 A:GLU592 4.1 27.6 1.0
NE2 A:HIS595 4.1 25.1 1.0
O A:HOH984 4.2 33.1 1.0
OG1 A:THR633 4.2 24.2 1.0
CD2 A:HIS567 4.3 26.5 1.0
CD2 A:HIS563 4.3 21.6 1.0
CB A:ASP564 4.4 25.1 1.0
CD2 A:HIS595 4.4 24.2 1.0
O A:HIS563 4.4 24.6 1.0
O A:THR633 4.4 27.1 1.0
NE2 A:HIS567 4.5 24.8 1.0
OD2 A:ASP674 4.5 31.6 1.0
CD2 A:HIS525 4.6 27.7 1.0
NE2 A:HIS525 4.6 28.6 1.0
NE2 A:HIS563 4.7 23.8 1.0
CB A:THR633 4.7 23.2 1.0
CA A:ASP564 4.8 24.9 1.0
CD A:GLU592 4.9 27.7 1.0
CG A:GLU592 4.9 25.9 1.0

Magnesium binding site 2 out of 4 in 5sez

Go back to Magnesium Binding Sites List in 5sez
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-6-Ethyl-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl) Pyridine-4-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 2- Chloro-6-Ethyl-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl) Pyridine-4-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:22.4
occ:1.00
 O B:HOH990 1.9 18.4 1.0
O B:HOH974 2.0 24.1 1.0
O B:HOH997 2.1 19.9 1.0
O B:HOH957 2.1 21.2 1.0
OD1 B:ASP564 2.1 23.8 1.0
O B:HOH1014 2.1 21.7 1.0
CG B:ASP564 3.1 22.7 1.0
OD2 B:ASP564 3.4 20.8 1.0
ZN B:ZN801 3.7 28.8 1.0
NE2 B:HIS595 4.0 25.5 1.0
O B:HOH945 4.0 34.8 1.0
O B:HOH1047 4.1 38.9 1.0
OE2 B:GLU592 4.1 26.9 1.0
OG1 B:THR633 4.2 21.5 1.0
CD2 B:HIS563 4.2 21.2 1.0
CD2 B:HIS595 4.3 23.8 1.0
O B:HOH983 4.3 28.0 1.0
CD2 B:HIS567 4.3 26.9 1.0
O B:HIS563 4.4 26.2 1.0
CB B:ASP564 4.4 22.5 1.0
OD2 B:ASP674 4.5 25.3 1.0
NE2 B:HIS567 4.5 23.3 1.0
NE2 B:HIS563 4.6 20.8 1.0
O B:THR633 4.6 23.4 1.0
CD2 B:HIS525 4.6 22.7 1.0
NE2 B:HIS525 4.7 26.0 1.0
CB B:THR633 4.7 25.2 1.0
CA B:ASP564 4.7 22.1 1.0
CG B:GLU592 4.9 25.2 1.0
CD B:GLU592 5.0 24.6 1.0

Magnesium binding site 3 out of 4 in 5sez

Go back to Magnesium Binding Sites List in 5sez
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-6-Ethyl-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl) Pyridine-4-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 2- Chloro-6-Ethyl-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl) Pyridine-4-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:23.7
occ:1.00
 O C:HOH973 2.0 21.5 1.0
O C:HOH935 2.0 25.3 1.0
OD1 C:ASP564 2.0 21.9 1.0
O C:HOH1001 2.0 24.0 1.0
O C:HOH1034 2.1 23.4 1.0
O C:HOH930 2.2 22.1 1.0
CG C:ASP564 3.0 23.4 1.0
OD2 C:ASP564 3.4 24.1 1.0
ZN C:ZN801 3.7 30.4 1.0
OE2 C:GLU592 4.0 29.7 1.0
O C:HOH985 4.0 31.1 1.0
O C:HOH1022 4.0 40.6 1.0
NE2 C:HIS595 4.1 25.6 1.0
O C:HOH994 4.2 27.5 1.0
OG1 C:THR633 4.2 24.3 1.0
CD2 C:HIS563 4.3 22.5 1.0
CD2 C:HIS567 4.3 27.0 1.0
O C:HIS563 4.3 24.9 1.0
OD2 C:ASP674 4.4 33.2 1.0
CD2 C:HIS595 4.4 23.1 1.0
CB C:ASP564 4.4 23.1 1.0
NE2 C:HIS567 4.5 26.7 1.0
O C:THR633 4.5 25.8 1.0
CD2 C:HIS525 4.6 27.3 1.0
NE2 C:HIS563 4.7 25.0 1.0
CB C:THR633 4.7 26.5 1.0
NE2 C:HIS525 4.7 28.4 1.0
CA C:ASP564 4.8 24.0 1.0
CD C:GLU592 4.8 27.1 1.0
CG C:GLU592 4.8 25.0 1.0

Magnesium binding site 4 out of 4 in 5sez

Go back to Magnesium Binding Sites List in 5sez
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Chloro-6-Ethyl-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl) Pyridine-4-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 2- Chloro-6-Ethyl-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7-Yl) Pyridine-4-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:32.5
occ:1.00
 O D:HOH942 2.0 24.1 1.0
O D:HOH968 2.1 27.7 1.0
O D:HOH963 2.1 25.8 1.0
O D:HOH926 2.1 29.8 1.0
OD1 D:ASP564 2.2 31.6 1.0
O D:HOH913 2.2 24.5 1.0
CG D:ASP564 3.1 29.9 1.0
OD2 D:ASP564 3.5 35.8 1.0
ZN D:ZN801 3.7 34.2 1.0
O D:HOH955 3.9 34.4 1.0
OE2 D:GLU592 4.1 32.9 1.0
NE2 D:HIS595 4.1 30.0 1.0
OG1 D:THR633 4.2 29.4 1.0
O D:HOH988 4.2 33.4 1.0
CD2 D:HIS563 4.2 28.9 1.0
OD2 D:ASP674 4.3 32.8 1.0
CD2 D:HIS595 4.4 30.0 1.0
O D:HIS563 4.4 30.1 1.0
CD2 D:HIS567 4.4 33.1 1.0
O D:THR633 4.4 34.7 1.0
CB D:ASP564 4.5 29.0 1.0
CD2 D:HIS525 4.6 32.8 1.0
NE2 D:HIS525 4.6 39.5 1.0
CB D:THR633 4.6 30.0 1.0
NE2 D:HIS567 4.6 29.1 1.0
NE2 D:HIS563 4.7 24.6 1.0
CA D:ASP564 4.9 27.1 1.0
CG D:GLU592 4.9 33.7 1.0
CD D:GLU592 4.9 36.4 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 03:27:57 2024

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