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Zinc in PDB 5sdu: Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Methyl-4-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2-Phenyl-1,3- Oxazole

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Methyl-4-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2-Phenyl-1,3- Oxazole

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Methyl-4-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2-Phenyl-1,3- Oxazole:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Methyl-4-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2-Phenyl-1,3- Oxazole, PDB code: 5sdu 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) 43.75 / 2.15
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.21, 135.21, 235.801, 90, 90, 120
R / Rfree (%) 19.3 / 23.5

Other elements in 5sdu:

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

Zinc binding site 1 out of 4 in 5sdu

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Methyl-4-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2-Phenyl-1,3- Oxazole


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 5- Methyl-4-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2-Phenyl-1,3- Oxazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:24.7
occ:1.00
 OD2 A:ASP564 2.1 21.5 1.0
NE2 A:HIS563 2.1 18.2 1.0
NE2 A:HIS529 2.1 21.9 1.0
OD1 A:ASP674 2.1 23.1 1.0
O A:HOH959 2.1 18.8 1.0
O A:HOH1000 2.3 24.5 1.0
CD2 A:HIS563 3.0 18.6 1.0
CG A:ASP674 3.0 24.6 1.0
CG A:ASP564 3.1 19.9 1.0
CD2 A:HIS529 3.1 20.7 1.0
CE1 A:HIS529 3.1 23.4 1.0
CE1 A:HIS563 3.2 19.8 1.0
OD2 A:ASP674 3.3 30.1 1.0
OD1 A:ASP564 3.6 18.5 1.0
MG A:MG802 3.8 22.1 1.0
O A:HOH1008 4.1 15.6 1.0
CG A:HIS563 4.1 19.0 1.0
CD2 A:HIS525 4.2 24.4 1.0
ND1 A:HIS563 4.2 19.3 1.0
CG A:HIS529 4.2 20.6 1.0
ND1 A:HIS529 4.2 22.1 1.0
O A:HOH937 4.2 24.3 1.0
CB A:ASP564 4.2 19.0 1.0
CB A:ASP674 4.4 23.5 1.0
NE2 A:HIS525 4.5 23.0 1.0
O A:HOH944 4.6 19.9 1.0
CG2 A:VAL533 4.7 18.3 1.0
CA A:ASP674 4.8 21.4 1.0
O A:ASP674 4.8 21.1 1.0

Zinc binding site 2 out of 4 in 5sdu

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


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 5- Methyl-4-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2-Phenyl-1,3- Oxazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:24.6
occ:1.00
 NE2 B:HIS563 2.1 15.5 1.0
O B:HOH942 2.1 14.8 1.0
OD2 B:ASP564 2.1 18.8 1.0
NE2 B:HIS529 2.1 20.6 1.0
OD1 B:ASP674 2.2 23.1 1.0
O B:HOH984 2.3 21.6 1.0
CG B:ASP674 3.0 23.1 1.0
CD2 B:HIS563 3.0 16.5 1.0
CD2 B:HIS529 3.1 20.8 1.0
CE1 B:HIS563 3.1 16.9 1.0
CG B:ASP564 3.1 18.2 1.0
OD2 B:ASP674 3.2 23.1 1.0
CE1 B:HIS529 3.2 21.4 1.0
OD1 B:ASP564 3.6 18.2 1.0
MG B:MG802 3.9 16.2 1.0
O B:HOH1007 4.0 17.2 1.0
CD2 B:HIS525 4.1 22.1 1.0
O B:HOH988 4.1 27.4 1.0
CG B:HIS563 4.2 16.6 1.0
ND1 B:HIS563 4.2 15.8 1.0
CG B:HIS529 4.2 21.0 1.0
ND1 B:HIS529 4.3 19.8 1.0
CB B:ASP564 4.3 18.3 1.0
O B:HOH1010 4.3 53.3 1.0
CB B:ASP674 4.4 21.8 1.0
NE2 B:HIS525 4.4 21.9 1.0
O B:HOH919 4.5 18.3 1.0
CG2 B:VAL533 4.7 19.1 1.0
CA B:ASP674 4.8 21.3 1.0

Zinc binding site 3 out of 4 in 5sdu

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


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 5- Methyl-4-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2-Phenyl-1,3- Oxazole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:26.8
occ:1.00
 NE2 C:HIS529 2.1 22.9 1.0
NE2 C:HIS563 2.1 17.5 1.0
O C:HOH976 2.1 19.6 1.0
OD2 C:ASP564 2.2 19.1 1.0
OD1 C:ASP674 2.2 23.2 1.0
O C:HOH1016 2.3 25.0 1.0
CD2 C:HIS563 3.0 18.5 1.0
CD2 C:HIS529 3.0 22.4 1.0
CG C:ASP674 3.1 24.1 1.0
CE1 C:HIS529 3.2 24.2 1.0
CE1 C:HIS563 3.2 19.4 1.0
CG C:ASP564 3.2 19.3 1.0
OD2 C:ASP674 3.4 28.6 1.0
OD1 C:ASP564 3.7 19.8 1.0
MG C:MG802 3.8 20.5 1.0
CD2 C:HIS525 4.2 22.9 1.0
CG C:HIS563 4.2 18.1 1.0
O C:HOH1007 4.2 25.5 1.0
CG C:HIS529 4.2 23.3 1.0
O C:HOH1027 4.2 16.4 1.0
ND1 C:HIS529 4.2 22.3 1.0
ND1 C:HIS563 4.2 17.3 1.0
CB C:ASP564 4.4 18.2 1.0
CB C:ASP674 4.5 24.3 1.0
O C:HOH1044 4.5 44.5 1.0
O C:HOH939 4.5 20.2 1.0
NE2 C:HIS525 4.6 22.5 1.0
CG2 C:VAL533 4.7 20.9 1.0
CA C:ASP674 4.8 23.4 1.0
O C:ASP674 4.9 24.5 1.0

Zinc binding site 4 out of 4 in 5sdu

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


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 5- Methyl-4-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2-Phenyl-1,3- Oxazole within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:35.7
occ:1.00
 O D:HOH925 2.1 19.8 1.0
NE2 D:HIS563 2.1 26.7 1.0
NE2 D:HIS529 2.2 30.6 1.0
OD1 D:ASP674 2.2 34.4 1.0
OD2 D:ASP564 2.2 39.6 1.0
O D:HOH965 2.2 32.5 1.0
CD2 D:HIS563 2.9 27.2 1.0
CG D:ASP674 3.1 34.5 1.0
CD2 D:HIS529 3.1 31.5 1.0
CG D:ASP564 3.2 32.6 1.0
CE1 D:HIS529 3.2 30.5 1.0
CE1 D:HIS563 3.3 28.9 1.0
OD2 D:ASP674 3.3 33.9 1.0
OD1 D:ASP564 3.7 31.8 1.0
MG D:MG802 3.8 31.2 1.0
CG D:HIS563 4.1 27.0 1.0
CD2 D:HIS525 4.2 35.0 1.0
O D:HOH975 4.2 26.4 1.0
O D:HOH940 4.2 36.6 1.0
CB D:ASP564 4.3 32.4 1.0
ND1 D:HIS563 4.3 26.4 1.0
ND1 D:HIS529 4.3 28.7 1.0
CG D:HIS529 4.3 31.1 1.0
O D:HOH915 4.4 30.5 1.0
CB D:ASP674 4.4 33.0 1.0
NE2 D:HIS525 4.6 36.6 1.0
CG2 D:VAL533 4.7 32.0 1.0
O D:ASP674 4.7 34.6 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 04:30:07 2024

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