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Zinc in PDB 5sf5: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazine

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

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]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-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazine, PDB code: 5sf5 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) 43.82 / 1.98
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.992, 135.992, 236.077, 90, 90, 120
R / Rfree (%) 17.8 / 22.3

Other elements in 5sf5:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]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-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazine (pdb code 5sf5). 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-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazine, PDB code: 5sf5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sf5

Go back to Zinc Binding Sites List in 5sf5
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]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-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:32.8
occ:1.00
 O A:HOH945 2.1 26.2 1.0
NE2 A:HIS529 2.1 31.8 1.0
O A:HOH987 2.1 29.1 1.0
OD2 A:ASP564 2.2 29.8 1.0
OD1 A:ASP674 2.2 30.9 1.0
NE2 A:HIS563 2.2 25.7 1.0
CD2 A:HIS563 3.0 23.8 1.0
CG A:ASP674 3.1 30.2 1.0
CD2 A:HIS529 3.1 28.6 1.0
CG A:ASP564 3.1 32.3 1.0
CE1 A:HIS529 3.1 30.9 1.0
CE1 A:HIS563 3.3 30.4 1.0
OD2 A:ASP674 3.4 34.6 1.0
OD1 A:ASP564 3.6 26.5 1.0
MG A:MG802 3.8 26.8 1.0
O A:HOH1026 4.1 26.1 1.0
CD2 A:HIS525 4.2 31.4 1.0
O A:HOH918 4.2 33.1 1.0
CG A:HIS563 4.2 26.7 1.0
ND1 A:HIS529 4.3 29.0 1.0
CG A:HIS529 4.3 31.1 1.0
CB A:ASP564 4.3 29.6 1.0
ND1 A:HIS563 4.3 28.3 1.0
NE2 A:HIS525 4.4 30.9 1.0
CB A:ASP674 4.4 28.5 1.0
O A:HOH931 4.6 22.9 1.0
CG2 A:VAL533 4.7 25.5 1.0
O A:ASP674 4.8 29.6 1.0
CA A:ASP674 4.9 27.2 1.0

Zinc binding site 2 out of 4 in 5sf5

Go back to Zinc Binding Sites List in 5sf5
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]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-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:31.6
occ:1.00
 O B:HOH969 2.1 20.6 1.0
OD1 B:ASP674 2.1 24.6 1.0
NE2 B:HIS563 2.2 25.4 1.0
NE2 B:HIS529 2.2 27.2 1.0
OD2 B:ASP564 2.2 26.3 1.0
O B:HOH981 2.3 32.1 1.0
CG B:ASP674 3.0 25.6 1.0
CD2 B:HIS563 3.1 24.6 1.0
CG B:ASP564 3.2 26.3 1.0
CD2 B:HIS529 3.2 27.2 1.0
CE1 B:HIS529 3.2 28.6 1.0
CE1 B:HIS563 3.2 24.7 1.0
OD2 B:ASP674 3.3 24.8 1.0
OD1 B:ASP564 3.6 25.5 1.0
MG B:MG802 3.8 24.5 1.0
O B:HOH950 4.0 33.2 1.0
O B:HOH1015 4.0 24.0 1.0
CD2 B:HIS525 4.1 26.8 1.0
CG B:HIS563 4.2 24.0 1.0
ND1 B:HIS563 4.3 25.4 1.0
ND1 B:HIS529 4.3 23.5 1.0
NE2 B:HIS525 4.3 29.8 1.0
CG B:HIS529 4.3 24.9 1.0
CB B:ASP564 4.4 24.6 1.0
CB B:ASP674 4.4 25.5 1.0
O B:HOH942 4.6 28.2 1.0
CG2 B:VAL533 4.8 23.3 1.0
O B:HOH1061 4.8 37.6 1.0
CA B:ASP674 4.9 23.6 1.0
O B:ASP674 4.9 26.3 1.0

Zinc binding site 3 out of 4 in 5sf5

Go back to Zinc Binding Sites List in 5sf5
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]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-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:32.8
occ:1.00
 O C:HOH946 2.1 24.4 1.0
NE2 C:HIS529 2.2 29.0 1.0
OD2 C:ASP564 2.2 24.8 1.0
OD1 C:ASP674 2.2 24.3 1.0
NE2 C:HIS563 2.2 27.6 1.0
O C:HOH968 2.3 35.5 1.0
CG C:ASP674 3.1 28.2 1.0
CD2 C:HIS529 3.1 28.5 1.0
CD2 C:HIS563 3.1 27.8 1.0
CG C:ASP564 3.2 24.3 1.0
CE1 C:HIS529 3.2 30.9 1.0
OD2 C:ASP674 3.3 33.0 1.0
CE1 C:HIS563 3.3 25.4 1.0
OD1 C:ASP564 3.6 25.5 1.0
MG C:MG802 3.8 29.0 1.0
CD2 C:HIS525 4.1 29.6 1.0
O C:HOH943 4.2 33.0 1.0
O C:HOH1024 4.2 26.0 1.0
CG C:HIS529 4.3 26.1 1.0
CG C:HIS563 4.3 25.7 1.0
ND1 C:HIS529 4.3 27.9 1.0
ND1 C:HIS563 4.3 29.7 1.0
NE2 C:HIS525 4.3 29.8 1.0
CB C:ASP564 4.4 23.6 1.0
CB C:ASP674 4.4 29.5 1.0
O C:HOH966 4.6 26.8 1.0
CG2 C:VAL533 4.8 27.8 1.0
O C:HOH1062 4.8 42.5 1.0
CA C:ASP674 4.8 30.5 1.0
O C:ASP674 4.9 27.2 1.0

Zinc binding site 4 out of 4 in 5sf5

Go back to Zinc Binding Sites List in 5sf5
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]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-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:39.1
occ:1.00
 O D:HOH953 2.0 29.6 1.0
O D:HOH982 2.1 33.6 1.0
NE2 D:HIS529 2.2 36.0 1.0
OD2 D:ASP564 2.2 38.9 1.0
NE2 D:HIS563 2.2 26.2 1.0
OD1 D:ASP674 2.3 35.2 1.0
CD2 D:HIS563 2.9 27.6 1.0
CG D:ASP674 3.1 37.9 1.0
CG D:ASP564 3.1 34.2 1.0
CD2 D:HIS529 3.1 39.9 1.0
CE1 D:HIS529 3.2 36.6 1.0
OD2 D:ASP674 3.3 41.7 1.0
CE1 D:HIS563 3.4 29.2 1.0
OD1 D:ASP564 3.6 37.2 1.0
MG D:MG802 3.8 37.8 1.0
O D:HOH934 4.1 46.3 1.0
CD2 D:HIS525 4.1 37.4 1.0
O D:HOH976 4.2 32.7 1.0
CG D:HIS563 4.2 27.8 1.0
ND1 D:HIS529 4.3 36.0 1.0
CB D:ASP564 4.3 34.5 1.0
CG D:HIS529 4.3 35.9 1.0
ND1 D:HIS563 4.4 29.8 1.0
NE2 D:HIS525 4.5 44.9 1.0
CB D:ASP674 4.5 36.8 1.0
O D:HOH905 4.5 36.9 1.0
CG2 D:VAL533 4.8 37.5 1.0
O D:ASP674 4.9 34.9 1.0
CA D:ASP674 4.9 34.5 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 04:50:43 2024

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