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Zinc in PDB 5sev: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine, PDB code: 5sev 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) 43.76 / 2.31
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.434, 135.434, 235.847, 90, 90, 120
R / Rfree (%) 17.9 / 23.1

Other elements in 5sev:

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

Zinc binding site 1 out of 4 in 5sev

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine


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 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:40.1
occ:1.00
 OD2 A:ASP564 2.0 37.7 1.0
NE2 A:HIS563 2.0 32.5 1.0
NE2 A:HIS529 2.1 35.9 1.0
O A:HOH962 2.2 27.1 1.0
OD1 A:ASP674 2.3 39.8 1.0
O A:HOH954 2.4 38.9 1.0
CD2 A:HIS563 2.9 31.2 1.0
CE1 A:HIS529 3.0 31.5 1.0
CE1 A:HIS563 3.1 35.1 1.0
CG A:ASP564 3.1 37.5 1.0
CD2 A:HIS529 3.1 35.5 1.0
CG A:ASP674 3.1 40.0 1.0
OD2 A:ASP674 3.3 52.3 1.0
OD1 A:ASP564 3.7 36.4 1.0
MG A:MG802 3.8 33.6 1.0
CG A:HIS563 4.1 30.8 1.0
ND1 A:HIS563 4.1 33.3 1.0
ND1 A:HIS529 4.2 32.0 1.0
CD2 A:HIS525 4.2 43.2 1.0
CG A:HIS529 4.2 32.9 1.0
CB A:ASP564 4.3 34.1 1.0
O A:HOH991 4.3 26.0 1.0
NE2 A:HIS525 4.5 39.5 1.0
O A:HOH907 4.5 41.4 1.0
CB A:ASP674 4.5 38.1 1.0
O A:HOH947 4.6 32.0 1.0
CG2 A:VAL533 4.7 31.4 1.0
O A:ASP674 4.9 40.8 1.0
CA A:ASP674 4.9 34.3 1.0

Zinc binding site 2 out of 4 in 5sev

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


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 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:39.4
occ:1.00
 NE2 B:HIS563 2.1 28.9 1.0
OD1 B:ASP674 2.1 35.6 1.0
OD2 B:ASP564 2.1 36.0 1.0
O B:HOH939 2.2 25.6 1.0
NE2 B:HIS529 2.2 33.6 1.0
O B:HOH970 2.3 43.5 1.0
CD2 B:HIS563 3.0 31.7 1.0
CG B:ASP674 3.0 36.9 1.0
CE1 B:HIS563 3.2 31.4 1.0
CD2 B:HIS529 3.2 33.3 1.0
CG B:ASP564 3.2 31.6 1.0
OD2 B:ASP674 3.2 37.6 1.0
CE1 B:HIS529 3.2 36.9 1.0
OD1 B:ASP564 3.6 31.9 1.0
MG B:MG802 3.8 32.5 1.0
CD2 B:HIS525 4.1 37.1 1.0
O B:HOH973 4.1 25.6 1.0
CG B:HIS563 4.2 28.4 1.0
ND1 B:HIS563 4.2 30.1 1.0
CG B:HIS529 4.3 33.8 1.0
ND1 B:HIS529 4.3 36.5 1.0
NE2 B:HIS525 4.4 38.1 1.0
CB B:ASP564 4.4 31.4 1.0
CB B:ASP674 4.4 37.2 1.0
O B:HOH957 4.5 42.7 1.0
O B:HOH922 4.6 31.3 1.0
CG2 B:VAL533 4.8 31.8 1.0
CA B:ASP674 4.8 33.1 1.0
O B:ASP674 5.0 34.5 1.0

Zinc binding site 3 out of 4 in 5sev

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


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 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:43.1
occ:1.00
 O C:HOH924 2.1 29.4 1.0
NE2 C:HIS563 2.1 35.8 1.0
OD2 C:ASP564 2.1 35.2 1.0
OD1 C:ASP674 2.2 40.2 1.0
NE2 C:HIS529 2.2 37.1 1.0
O C:HOH973 2.4 41.5 1.0
CD2 C:HIS563 3.0 33.5 1.0
CG C:ASP674 3.1 38.3 1.0
CD2 C:HIS529 3.1 34.8 1.0
CE1 C:HIS529 3.2 36.5 1.0
CG C:ASP564 3.2 34.9 1.0
CE1 C:HIS563 3.2 35.7 1.0
OD2 C:ASP674 3.4 38.2 1.0
OD1 C:ASP564 3.7 34.6 1.0
MG C:MG802 3.8 34.5 1.0
CD2 C:HIS525 4.1 43.2 1.0
O C:HOH977 4.1 34.8 1.0
CG C:HIS563 4.2 34.1 1.0
ND1 C:HIS563 4.2 30.7 1.0
ND1 C:HIS529 4.3 34.4 1.0
CG C:HIS529 4.3 37.3 1.0
CB C:ASP564 4.3 32.4 1.0
NE2 C:HIS525 4.4 41.2 1.0
CB C:ASP674 4.5 39.5 1.0
O C:HOH955 4.5 50.4 1.0
O C:HOH919 4.6 37.0 1.0
CG2 C:VAL533 4.7 32.9 1.0
O C:HOH992 4.7 54.5 1.0
CA C:ASP674 4.8 37.2 1.0

Zinc binding site 4 out of 4 in 5sev

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Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine


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 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:51.8
occ:1.00
 OD2 D:ASP564 2.1 56.4 1.0
NE2 D:HIS563 2.1 41.9 1.0
OD1 D:ASP674 2.2 54.2 1.0
NE2 D:HIS529 2.2 49.9 1.0
O D:HOH919 2.2 39.4 1.0
O D:HOH925 2.4 42.9 1.0
CD2 D:HIS563 2.9 39.5 1.0
CG D:ASP674 3.0 51.4 1.0
CD2 D:HIS529 3.1 51.4 1.0
CG D:ASP564 3.1 44.8 1.0
CE1 D:HIS563 3.2 42.4 1.0
OD2 D:ASP674 3.3 54.5 1.0
CE1 D:HIS529 3.3 54.5 1.0
OD1 D:ASP564 3.7 50.2 1.0
MG D:MG802 3.9 44.5 1.0
O D:HOH934 4.1 39.3 1.0
CG D:HIS563 4.1 41.7 1.0
CD2 D:HIS525 4.2 48.8 1.0
ND1 D:HIS563 4.2 41.2 1.0
CB D:ASP564 4.3 45.9 1.0
O D:HOH924 4.3 47.9 1.0
CG D:HIS529 4.3 46.5 1.0
ND1 D:HIS529 4.3 48.8 1.0
O D:HOH921 4.4 43.3 1.0
CB D:ASP674 4.4 54.0 1.0
NE2 D:HIS525 4.5 53.0 1.0
CG2 D:VAL533 4.7 48.2 1.0
CA D:ASP674 4.8 49.3 1.0
O D:ASP674 4.8 54.0 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 04:46:48 2024

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