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Zinc in PDB 5sem: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine

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

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine, PDB code: 5sem 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) 43.57 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.449, 135.449, 235.505, 90, 90, 120
R / Rfree (%) 17.8 / 22.8

Other elements in 5sem:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine (pdb code 5sem). 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 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine, PDB code: 5sem:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sem

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine


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 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:38.2
occ:1.00
 O A:HOH984 2.1 29.4 1.0
O A:HOH982 2.1 35.2 1.0
OD1 A:ASP674 2.2 38.6 1.0
NE2 A:HIS529 2.2 34.7 1.0
NE2 A:HIS563 2.2 34.5 1.0
OD2 A:ASP564 2.2 37.8 1.0
CD2 A:HIS563 3.0 32.9 1.0
CG A:ASP674 3.1 37.3 1.0
CD2 A:HIS529 3.1 33.5 1.0
CG A:ASP564 3.1 32.4 1.0
CE1 A:HIS529 3.2 31.0 1.0
CE1 A:HIS563 3.3 36.6 1.0
OD2 A:ASP674 3.4 38.6 1.0
OD1 A:ASP564 3.6 29.7 1.0
MG A:MG802 3.8 32.3 1.0
O A:HOH999 4.1 27.8 1.0
CD2 A:HIS525 4.1 38.2 1.0
CG A:HIS563 4.2 32.5 1.0
O A:HOH950 4.2 35.5 1.0
ND1 A:HIS563 4.3 32.6 1.0
CG A:HIS529 4.3 32.9 1.0
ND1 A:HIS529 4.3 30.6 1.0
CB A:ASP564 4.3 30.2 1.0
NE2 A:HIS525 4.4 37.8 1.0
CB A:ASP674 4.4 35.9 1.0
O A:HOH917 4.6 27.4 1.0
CG2 A:VAL533 4.7 29.4 1.0
O A:HOH1011 4.8 48.6 1.0
O A:ASP674 4.9 35.6 1.0
CA A:ASP674 4.9 34.0 1.0

Zinc binding site 2 out of 4 in 5sem

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine


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 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:35.5
occ:1.00
 OD1 B:ASP674 2.1 28.7 1.0
O B:HOH979 2.1 25.1 1.0
NE2 B:HIS529 2.2 26.8 1.0
NE2 B:HIS563 2.2 26.9 1.0
OD2 B:ASP564 2.2 29.1 1.0
O B:HOH952 2.3 34.1 1.0
CG B:ASP674 3.1 29.8 1.0
CD2 B:HIS563 3.1 28.5 1.0
CD2 B:HIS529 3.1 31.6 1.0
CE1 B:HIS529 3.2 28.1 1.0
CG B:ASP564 3.2 27.2 1.0
CE1 B:HIS563 3.2 31.0 1.0
OD2 B:ASP674 3.3 30.9 1.0
OD1 B:ASP564 3.7 29.6 1.0
MG B:MG802 3.8 28.7 1.0
O B:HOH999 4.0 25.3 1.0
O B:HOH938 4.0 31.9 1.0
CD2 B:HIS525 4.1 29.6 1.0
CG B:HIS563 4.3 27.3 1.0
CG B:HIS529 4.3 28.5 1.0
ND1 B:HIS529 4.3 27.0 1.0
ND1 B:HIS563 4.3 28.8 1.0
NE2 B:HIS525 4.4 33.0 1.0
CB B:ASP564 4.4 26.5 1.0
CB B:ASP674 4.4 31.7 1.0
O B:HOH1022 4.4 45.2 1.0
O B:HOH945 4.7 30.1 1.0
CG2 B:VAL533 4.7 28.3 1.0
CA B:ASP674 4.9 27.9 1.0
O B:ASP674 4.9 30.9 1.0

Zinc binding site 3 out of 4 in 5sem

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Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine


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 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:37.1
occ:1.00
 O C:HOH971 2.1 29.1 1.0
NE2 C:HIS529 2.2 33.7 1.0
OD1 C:ASP674 2.2 29.0 1.0
NE2 C:HIS563 2.2 32.1 1.0
OD2 C:ASP564 2.2 30.1 1.0
O C:HOH964 2.3 35.1 1.0
CD2 C:HIS563 3.0 28.8 1.0
CG C:ASP674 3.1 30.6 1.0
CD2 C:HIS529 3.1 33.3 1.0
CG C:ASP564 3.2 30.6 1.0
CE1 C:HIS529 3.2 34.5 1.0
CE1 C:HIS563 3.3 27.2 1.0
OD2 C:ASP674 3.3 36.4 1.0
OD1 C:ASP564 3.7 29.6 1.0
MG C:MG802 3.8 32.2 1.0
CD2 C:HIS525 4.1 36.4 1.0
O C:HOH955 4.1 32.2 1.0
CG C:HIS563 4.2 29.5 1.0
O C:HOH1009 4.3 30.0 1.0
CG C:HIS529 4.3 30.1 1.0
ND1 C:HIS529 4.3 30.6 1.0
ND1 C:HIS563 4.3 30.1 1.0
NE2 C:HIS525 4.3 34.9 1.0
CB C:ASP564 4.4 29.0 1.0
CB C:ASP674 4.4 31.7 1.0
O C:HOH933 4.5 34.3 1.0
O C:HOH1016 4.7 44.8 1.0
CA C:ASP674 4.8 32.6 1.0
CG2 C:VAL533 4.8 30.2 1.0
O C:ASP674 4.9 34.8 1.0

Zinc binding site 4 out of 4 in 5sem

Go back to Zinc Binding Sites List in 5sem
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine


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 3- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:46.1
occ:1.00
 O D:HOH940 2.1 33.7 1.0
OD2 D:ASP564 2.2 49.7 1.0
NE2 D:HIS563 2.2 32.0 1.0
O D:HOH923 2.2 42.4 1.0
NE2 D:HIS529 2.2 39.1 1.0
OD1 D:ASP674 2.3 39.3 1.0
CD2 D:HIS563 2.9 35.2 1.0
CG D:ASP564 3.1 39.4 1.0
CG D:ASP674 3.1 41.5 1.0
CD2 D:HIS529 3.2 45.9 1.0
CE1 D:HIS529 3.3 41.2 1.0
OD2 D:ASP674 3.3 46.1 1.0
CE1 D:HIS563 3.4 35.7 1.0
OD1 D:ASP564 3.6 40.8 1.0
MG D:MG802 3.7 43.4 1.0
CD2 D:HIS525 4.0 45.2 1.0
O D:HOH910 4.1 50.4 1.0
O D:HOH950 4.2 40.3 1.0
CG D:HIS563 4.2 31.9 1.0
CB D:ASP564 4.3 41.4 1.0
NE2 D:HIS525 4.3 49.6 1.0
CG D:HIS529 4.3 41.1 1.0
ND1 D:HIS529 4.4 41.1 1.0
ND1 D:HIS563 4.4 35.7 1.0
O D:HOH908 4.4 36.9 1.0
CB D:ASP674 4.5 39.4 1.0
CG2 D:VAL533 4.7 43.4 1.0
O D:ASP674 4.8 43.2 1.0
CA D:ASP674 4.9 38.8 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: Fri Apr 7 21:47:00 2023

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