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Zinc in PDB 5sdx: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine, PDB code: 5sdx 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) 43.68 / 2.19
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.377, 135.377, 235.362, 90, 90, 120
R / Rfree (%) 18.7 / 24.3

Other elements in 5sdx:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine (pdb code 5sdx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine, PDB code: 5sdx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sdx

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:36.9
occ:1.00
 OD2 A:ASP564 2.0 33.1 1.0
O A:HOH970 2.1 32.0 1.0
O A:HOH956 2.1 25.7 1.0
OD1 A:ASP674 2.1 36.6 1.0
NE2 A:HIS563 2.1 29.0 1.0
NE2 A:HIS529 2.2 39.8 1.0
CD2 A:HIS563 3.0 31.6 1.0
CG A:ASP674 3.0 34.1 1.0
CG A:ASP564 3.0 31.7 1.0
CE1 A:HIS529 3.1 40.7 1.0
CD2 A:HIS529 3.1 38.2 1.0
CE1 A:HIS563 3.2 37.0 1.0
OD2 A:ASP674 3.2 44.4 1.0
OD1 A:ASP564 3.6 29.8 1.0
MG A:MG802 3.8 30.7 1.0
O A:HOH981 4.1 29.4 1.0
CD2 A:HIS525 4.1 37.8 1.0
CG A:HIS563 4.2 27.9 1.0
CB A:ASP564 4.2 32.0 1.0
ND1 A:HIS529 4.2 37.3 1.0
CG A:HIS529 4.3 37.6 1.0
ND1 A:HIS563 4.3 29.0 1.0
O A:HOH923 4.4 38.4 1.0
CB A:ASP674 4.4 37.0 1.0
NE2 A:HIS525 4.4 34.9 1.0
O A:HOH904 4.5 30.1 1.0
CG2 A:VAL533 4.7 24.0 1.0
O A:ASP674 4.8 34.4 1.0
CA A:ASP674 4.8 31.4 1.0

Zinc binding site 2 out of 4 in 5sdx

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:35.2
occ:1.00
 OD2 B:ASP564 2.1 34.7 1.0
NE2 B:HIS563 2.1 28.4 1.0
O B:HOH943 2.1 23.0 1.0
OD1 B:ASP674 2.1 32.5 1.0
O B:HOH970 2.2 29.3 1.0
NE2 B:HIS529 2.2 28.4 1.0
CG B:ASP674 3.0 30.9 1.0
CD2 B:HIS563 3.0 25.9 1.0
CG B:ASP564 3.1 29.8 1.0
CD2 B:HIS529 3.1 29.7 1.0
OD2 B:ASP674 3.1 34.1 1.0
CE1 B:HIS563 3.1 31.2 1.0
CE1 B:HIS529 3.3 35.2 1.0
OD1 B:ASP564 3.5 28.1 1.0
MG B:MG802 3.8 25.4 1.0
O B:HOH973 3.9 25.8 1.0
CD2 B:HIS525 4.1 32.2 1.0
O B:HOH978 4.1 37.5 1.0
CG B:HIS563 4.2 28.0 1.0
O B:HOH986 4.2 51.1 1.0
ND1 B:HIS563 4.2 27.1 1.0
CG B:HIS529 4.3 28.8 1.0
CB B:ASP564 4.3 27.5 1.0
NE2 B:HIS525 4.3 29.1 1.0
CB B:ASP674 4.4 31.7 1.0
ND1 B:HIS529 4.4 28.4 1.0
O B:HOH930 4.5 25.3 1.0
CG2 B:VAL533 4.8 25.7 1.0
CA B:ASP674 4.9 31.3 1.0
O B:ASP674 5.0 31.8 1.0

Zinc binding site 3 out of 4 in 5sdx

Go back to Zinc Binding Sites List in 5sdx
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:37.2
occ:1.00
 O C:HOH929 1.9 25.5 1.0
OD2 C:ASP564 2.1 32.3 1.0
NE2 C:HIS563 2.2 34.7 1.0
O C:HOH973 2.2 36.0 1.0
NE2 C:HIS529 2.2 34.7 1.0
OD1 C:ASP674 2.2 37.0 1.0
CG C:ASP674 3.0 32.6 1.0
CD2 C:HIS563 3.0 29.1 1.0
CD2 C:HIS529 3.1 30.9 1.0
CG C:ASP564 3.2 30.9 1.0
CE1 C:HIS529 3.2 36.5 1.0
OD2 C:ASP674 3.2 38.0 1.0
CE1 C:HIS563 3.2 30.5 1.0
OD1 C:ASP564 3.7 31.7 1.0
MG C:MG802 3.8 29.9 1.0
CD2 C:HIS525 4.1 35.8 1.0
O C:HOH980 4.1 29.9 1.0
O C:HOH964 4.2 34.9 1.0
CG C:HIS563 4.2 30.5 1.0
CG C:HIS529 4.3 33.4 1.0
ND1 C:HIS563 4.3 27.2 1.0
ND1 C:HIS529 4.3 31.5 1.0
CB C:ASP564 4.3 26.6 1.0
NE2 C:HIS525 4.4 34.6 1.0
CB C:ASP674 4.4 36.2 1.0
O C:HOH924 4.6 33.0 1.0
CG2 C:VAL533 4.7 29.5 1.0
CA C:ASP674 4.8 35.5 1.0
O C:ASP674 4.9 33.4 1.0

Zinc binding site 4 out of 4 in 5sdx

Go back to Zinc Binding Sites List in 5sdx
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:45.7
occ:1.00
 O D:HOH925 2.1 28.9 1.0
O D:HOH945 2.1 39.3 1.0
NE2 D:HIS563 2.1 34.3 1.0
NE2 D:HIS529 2.2 44.8 1.0
OD2 D:ASP564 2.2 45.6 1.0
OD1 D:ASP674 2.3 44.4 1.0
CD2 D:HIS563 3.0 39.4 1.0
CG D:ASP564 3.1 37.2 1.0
CG D:ASP674 3.1 41.6 1.0
CE1 D:HIS529 3.1 46.0 1.0
CD2 D:HIS529 3.2 45.8 1.0
CE1 D:HIS563 3.2 35.3 1.0
OD2 D:ASP674 3.3 42.2 1.0
OD1 D:ASP564 3.7 39.7 1.0
MG D:MG802 3.8 44.0 1.0
O D:HOH941 3.9 39.7 1.0
O D:HOH907 4.2 42.9 1.0
CG D:HIS563 4.2 34.0 1.0
CB D:ASP564 4.2 37.1 1.0
CD2 D:HIS525 4.2 44.5 1.0
ND1 D:HIS529 4.3 43.8 1.0
ND1 D:HIS563 4.3 37.3 1.0
CG D:HIS529 4.3 38.1 1.0
O D:HOH926 4.4 37.5 1.0
CB D:ASP674 4.5 44.1 1.0
NE2 D:HIS525 4.6 45.6 1.0
CG2 D:VAL533 4.7 48.9 1.0
O D:ASP674 4.8 45.2 1.0
CA D:ASP674 4.9 39.0 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: Mon Oct 28 04:31:07 2024

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