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Magnesium in PDB 5sea: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide, PDB code: 5sea 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) 41.66 / 2.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 136.069, 136.069, 235.628, 90, 90, 120
R / Rfree (%) 19.5 / 22.8

Other elements in 5sea:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 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-(2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide (pdb code 5sea). 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-(2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide, PDB code: 5sea:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sea

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

b:23.8
occ:1.00
 O A:HOH1004 2.0 22.0 1.0
O A:HOH951 2.0 21.5 1.0
O A:HOH920 2.0 22.4 1.0
OD1 A:ASP564 2.1 22.4 1.0
O A:HOH942 2.1 21.5 1.0
O A:HOH947 2.2 16.7 1.0
CG A:ASP564 3.1 23.8 1.0
OD2 A:ASP564 3.4 22.7 1.0
ZN A:ZN801 3.8 28.0 1.0
O A:HOH961 3.9 35.1 1.0
OE2 A:GLU592 4.0 27.4 1.0
NE2 A:HIS595 4.1 24.4 1.0
CD2 A:HIS567 4.2 26.5 1.0
O A:HOH1024 4.2 56.0 1.0
NE2 A:HIS567 4.4 29.0 1.0
CD2 A:HIS595 4.4 23.3 1.0
OG1 A:THR633 4.4 24.4 1.0
CB A:ASP564 4.4 24.5 1.0
O A:HOH986 4.5 37.4 1.0
CD2 A:HIS563 4.5 22.2 1.0
OD2 A:ASP674 4.5 30.5 1.0
CD2 A:HIS525 4.5 26.9 1.0
O A:HIS563 4.5 24.4 1.0
NE2 A:HIS525 4.5 26.5 1.0
O A:THR633 4.6 26.1 1.0
CB A:THR633 4.8 23.6 1.0
CA A:ASP564 4.8 24.4 1.0
NE2 A:HIS563 4.9 24.1 1.0
CD A:GLU592 4.9 28.0 1.0
CG A:GLU592 4.9 26.4 1.0

Magnesium binding site 2 out of 4 in 5sea

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

b:22.0
occ:1.00
 O B:HOH965 1.9 18.5 1.0
O B:HOH950 1.9 19.5 1.0
O B:HOH1028 2.1 20.8 1.0
O B:HOH994 2.1 17.8 1.0
OD1 B:ASP564 2.1 20.2 1.0
O B:HOH945 2.1 19.1 1.0
CG B:ASP564 3.1 21.8 1.0
OD2 B:ASP564 3.4 21.3 1.0
ZN B:ZN801 3.7 27.0 1.0
NE2 B:HIS595 4.1 23.5 1.0
O B:HOH963 4.1 37.0 1.0
O B:HOH1046 4.1 51.7 1.0
CD2 B:HIS563 4.2 19.7 1.0
OG1 B:THR633 4.2 22.1 1.0
OE2 B:GLU592 4.2 25.9 1.0
O B:HIS563 4.2 21.8 1.0
CD2 B:HIS595 4.3 24.4 1.0
CD2 B:HIS567 4.3 24.0 1.0
OD2 B:ASP674 4.4 25.8 1.0
O B:HOH957 4.4 30.1 1.0
CB B:ASP564 4.4 22.2 1.0
NE2 B:HIS567 4.5 22.9 1.0
O B:THR633 4.6 22.8 1.0
NE2 B:HIS563 4.6 19.9 1.0
CB B:THR633 4.6 22.6 1.0
CD2 B:HIS525 4.7 25.3 1.0
CA B:ASP564 4.7 22.4 1.0
NE2 B:HIS525 4.8 25.7 1.0
CG B:GLU592 4.8 24.2 1.0
CD B:GLU592 4.9 24.1 1.0

Magnesium binding site 3 out of 4 in 5sea

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

b:24.2
occ:1.00
 OD1 C:ASP564 2.0 23.2 1.0
O C:HOH1037 2.0 22.0 1.0
O C:HOH949 2.1 20.5 1.0
O C:HOH988 2.1 21.9 1.0
O C:HOH941 2.1 24.4 1.0
O C:HOH943 2.2 18.8 1.0
CG C:ASP564 3.0 23.2 1.0
OD2 C:ASP564 3.4 23.4 1.0
ZN C:ZN801 3.8 28.6 1.0
O C:HOH1009 3.9 36.8 1.0
OE2 C:GLU592 4.0 26.5 1.0
NE2 C:HIS595 4.1 24.1 1.0
OG1 C:THR633 4.2 23.6 1.0
CD2 C:HIS563 4.2 24.4 1.0
CD2 C:HIS567 4.3 26.1 1.0
O C:HIS563 4.3 23.1 1.0
O C:HOH1047 4.3 54.7 1.0
OD2 C:ASP674 4.3 32.9 1.0
CD2 C:HIS595 4.3 23.6 1.0
CB C:ASP564 4.4 22.6 1.0
O C:HOH1011 4.4 36.1 1.0
O C:THR633 4.5 25.1 1.0
NE2 C:HIS567 4.5 26.8 1.0
CB C:THR633 4.6 24.3 1.0
NE2 C:HIS563 4.7 25.2 1.0
CD2 C:HIS525 4.8 27.0 1.0
CA C:ASP564 4.8 22.9 1.0
NE2 C:HIS525 4.8 28.8 1.0
CG C:GLU592 4.8 24.1 1.0
CD C:GLU592 4.9 25.1 1.0

Magnesium binding site 4 out of 4 in 5sea

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

b:31.8
occ:1.00
 O D:HOH928 2.1 24.0 1.0
O D:HOH914 2.1 27.1 1.0
OD1 D:ASP564 2.1 26.6 1.0
O D:HOH966 2.1 19.5 1.0
O D:HOH988 2.2 25.7 1.0
O D:HOH913 2.2 23.5 1.0
CG D:ASP564 3.1 25.6 1.0
OD2 D:ASP564 3.5 28.6 1.0
ZN D:ZN801 3.8 32.4 1.0
O D:HOH980 3.8 40.6 1.0
NE2 D:HIS595 4.0 29.1 1.0
OE2 D:GLU592 4.1 33.3 1.0
OG1 D:THR633 4.2 28.6 1.0
CD2 D:HIS567 4.2 31.1 1.0
O D:HOH950 4.2 39.9 1.0
CD2 D:HIS563 4.2 24.9 1.0
O D:HIS563 4.3 26.6 1.0
CD2 D:HIS595 4.3 28.4 1.0
NE2 D:HIS567 4.4 30.8 1.0
OD2 D:ASP674 4.4 29.6 1.0
CB D:ASP564 4.5 26.0 1.0
O D:THR633 4.6 32.1 1.0
CD2 D:HIS525 4.6 34.8 1.0
NE2 D:HIS563 4.6 22.3 1.0
CB D:THR633 4.7 29.1 1.0
CA D:ASP564 4.8 27.0 1.0
NE2 D:HIS525 4.8 34.6 1.0
CG D:GLU592 4.8 34.4 1.0
CD D:GLU592 4.9 34.6 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 03:20:13 2024

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