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Zinc in PDB 5se9: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Imidazo[1,2- B]Pyridazine

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

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

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Imidazo[1,2- B]Pyridazine, PDB code: 5se9 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) 43.74 / 1.94
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.599, 135.599, 235.637, 90, 90, 120
R / Rfree (%) 17.5 / 21.9

Other elements in 5se9:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Imidazo[1,2- B]Pyridazine 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 2,3- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Imidazo[1,2- B]Pyridazine (pdb code 5se9). 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 2,3- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Imidazo[1,2- B]Pyridazine, PDB code: 5se9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5se9

Go back to Zinc Binding Sites List in 5se9
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]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 2,3- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Imidazo[1,2- B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:31.2
occ:1.00
 O A:HOH984 2.0 30.5 1.0
O A:HOH1005 2.1 24.1 1.0
OD2 A:ASP564 2.2 26.8 1.0
NE2 A:HIS529 2.2 28.0 1.0
NE2 A:HIS563 2.2 27.5 1.0
OD1 A:ASP674 2.2 29.3 1.0
CD2 A:HIS563 3.0 23.6 1.0
CD2 A:HIS529 3.1 26.2 1.0
CG A:ASP674 3.1 28.5 1.0
CG A:ASP564 3.1 27.8 1.0
CE1 A:HIS563 3.3 27.5 1.0
CE1 A:HIS529 3.3 28.2 1.0
OD2 A:ASP674 3.4 29.9 1.0
OD1 A:ASP564 3.6 25.5 1.0
MG A:MG802 3.8 26.4 1.0
O A:HOH1034 4.0 26.4 1.0
CD2 A:HIS525 4.2 27.8 1.0
CG A:HIS563 4.2 25.1 1.0
O A:HOH973 4.2 34.8 1.0
CG A:HIS529 4.3 28.1 1.0
ND1 A:HIS563 4.3 27.9 1.0
ND1 A:HIS529 4.3 25.2 1.0
CB A:ASP564 4.4 26.7 1.0
NE2 A:HIS525 4.5 29.6 1.0
CB A:ASP674 4.5 27.2 1.0
O A:HOH931 4.6 23.7 1.0
O A:HOH1050 4.7 40.9 1.0
CG2 A:VAL533 4.7 23.7 1.0
CA A:ASP674 4.9 25.3 1.0
O A:ASP674 4.9 25.3 1.0

Zinc binding site 2 out of 4 in 5se9

Go back to Zinc Binding Sites List in 5se9
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]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 2,3- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Imidazo[1,2- B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:29.8
occ:1.00
 O B:HOH959 2.1 20.6 1.0
OD1 B:ASP674 2.1 22.2 1.0
O B:HOH1012 2.2 29.5 1.0
NE2 B:HIS563 2.2 23.0 1.0
NE2 B:HIS529 2.2 23.2 1.0
OD2 B:ASP564 2.2 22.8 1.0
CG B:ASP674 3.0 25.8 1.0
CD2 B:HIS563 3.1 22.7 1.0
CG B:ASP564 3.2 22.7 1.0
CD2 B:HIS529 3.2 26.0 1.0
CE1 B:HIS529 3.2 27.1 1.0
CE1 B:HIS563 3.2 22.3 1.0
OD2 B:ASP674 3.3 24.5 1.0
OD1 B:ASP564 3.6 23.0 1.0
MG B:MG802 3.8 23.9 1.0
O B:HOH1018 4.0 22.4 1.0
CD2 B:HIS525 4.1 26.2 1.0
O B:HOH991 4.1 31.4 1.0
CG B:HIS563 4.2 23.2 1.0
ND1 B:HIS529 4.3 22.7 1.0
ND1 B:HIS563 4.3 21.7 1.0
CG B:HIS529 4.3 24.5 1.0
CB B:ASP564 4.3 21.9 1.0
NE2 B:HIS525 4.4 28.3 1.0
CB B:ASP674 4.4 25.8 1.0
O B:HOH946 4.6 23.8 1.0
O B:HOH1067 4.7 41.0 1.0
CG2 B:VAL533 4.7 21.5 1.0
CA B:ASP674 4.9 24.1 1.0
O B:ASP674 5.0 24.8 1.0

Zinc binding site 3 out of 4 in 5se9

Go back to Zinc Binding Sites List in 5se9
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]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 2,3- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Imidazo[1,2- B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:30.6
occ:1.00
 O C:HOH958 2.0 22.8 1.0
OD2 C:ASP564 2.1 24.7 1.0
OD1 C:ASP674 2.2 25.4 1.0
NE2 C:HIS529 2.2 26.2 1.0
NE2 C:HIS563 2.2 22.7 1.0
O C:HOH1006 2.3 28.4 1.0
CG C:ASP674 3.0 25.8 1.0
CD2 C:HIS563 3.1 22.1 1.0
CD2 C:HIS529 3.1 25.4 1.0
CG C:ASP564 3.1 25.7 1.0
OD2 C:ASP674 3.3 31.3 1.0
CE1 C:HIS563 3.3 22.1 1.0
CE1 C:HIS529 3.3 26.7 1.0
OD1 C:ASP564 3.6 22.5 1.0
MG C:MG802 3.8 25.5 1.0
CD2 C:HIS525 4.1 28.2 1.0
O C:HOH1050 4.1 25.6 1.0
CG C:HIS563 4.3 22.3 1.0
O C:HOH995 4.3 33.3 1.0
CG C:HIS529 4.3 24.1 1.0
ND1 C:HIS563 4.3 26.7 1.0
CB C:ASP564 4.4 22.1 1.0
ND1 C:HIS529 4.4 22.9 1.0
NE2 C:HIS525 4.4 28.3 1.0
CB C:ASP674 4.4 26.5 1.0
O C:HOH1064 4.5 42.7 1.0
O C:HOH953 4.5 24.9 1.0
CG2 C:VAL533 4.8 26.9 1.0
CA C:ASP674 4.8 28.9 1.0
O C:ASP674 4.9 28.0 1.0

Zinc binding site 4 out of 4 in 5se9

Go back to Zinc Binding Sites List in 5se9
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]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 2,3- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Imidazo[1,2- B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:37.4
occ:1.00
 O D:HOH937 2.0 26.9 1.0
O D:HOH974 2.1 36.5 1.0
NE2 D:HIS563 2.1 29.6 1.0
NE2 D:HIS529 2.2 36.6 1.0
OD2 D:ASP564 2.2 35.0 1.0
OD1 D:ASP674 2.2 31.7 1.0
CD2 D:HIS563 2.9 34.5 1.0
CG D:ASP674 3.1 35.1 1.0
CG D:ASP564 3.1 29.3 1.0
CD2 D:HIS529 3.2 39.4 1.0
CE1 D:HIS529 3.2 36.2 1.0
CE1 D:HIS563 3.3 31.5 1.0
OD2 D:ASP674 3.3 35.6 1.0
OD1 D:ASP564 3.6 34.1 1.0
MG D:MG802 3.7 34.6 1.0
CD2 D:HIS525 4.1 35.2 1.0
CG D:HIS563 4.1 28.9 1.0
O D:HOH961 4.2 28.8 1.0
O D:HOH923 4.2 34.8 1.0
ND1 D:HIS563 4.3 30.4 1.0
CB D:ASP564 4.3 30.0 1.0
ND1 D:HIS529 4.3 34.3 1.0
CG D:HIS529 4.3 33.3 1.0
NE2 D:HIS525 4.4 41.0 1.0
CB D:ASP674 4.5 33.8 1.0
O D:HOH915 4.7 33.4 1.0
CG2 D:VAL533 4.8 36.9 1.0
O D:ASP674 4.9 33.3 1.0
CA D:ASP674 4.9 32.7 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 04:37:42 2024

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