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Zinc in PDB 5sep: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (4-Cyclopentyl-1-Methylimidazol-2-Yl)Ethyl]-5,8-Dimethyl-[1,2, 4]Triazolo[1,5-A]Pyrazine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (4-Cyclopentyl-1-Methylimidazol-2-Yl)Ethyl]-5,8-Dimethyl-[1,2, 4]Triazolo[1,5-A]Pyrazine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (4-Cyclopentyl-1-Methylimidazol-2-Yl)Ethyl]-5,8-Dimethyl-[1,2, 4]Triazolo[1,5-A]Pyrazine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (4-Cyclopentyl-1-Methylimidazol-2-Yl)Ethyl]-5,8-Dimethyl-[1,2, 4]Triazolo[1,5-A]Pyrazine, PDB code: 5sep 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) 43.53 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.31, 135.31, 235.458, 90, 90, 120
R / Rfree (%) 17.4 / 22.6

Other elements in 5sep:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (4-Cyclopentyl-1-Methylimidazol-2-Yl)Ethyl]-5,8-Dimethyl-[1,2, 4]Triazolo[1,5-A]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-[2- (4-Cyclopentyl-1-Methylimidazol-2-Yl)Ethyl]-5,8-Dimethyl-[1,2, 4]Triazolo[1,5-A]Pyrazine (pdb code 5sep). 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-[2- (4-Cyclopentyl-1-Methylimidazol-2-Yl)Ethyl]-5,8-Dimethyl-[1,2, 4]Triazolo[1,5-A]Pyrazine, PDB code: 5sep:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sep

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (4-Cyclopentyl-1-Methylimidazol-2-Yl)Ethyl]-5,8-Dimethyl-[1,2, 4]Triazolo[1,5-A]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-[2- (4-Cyclopentyl-1-Methylimidazol-2-Yl)Ethyl]-5,8-Dimethyl-[1,2, 4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:37.0
occ:1.00
 O A:HOH991 2.1 32.5 1.0
NE2 A:HIS529 2.1 38.2 1.0
OD2 A:ASP564 2.2 35.6 1.0
NE2 A:HIS563 2.2 30.2 1.0
OD1 A:ASP674 2.2 33.7 1.0
O A:HOH995 2.4 42.5 1.0
CD2 A:HIS563 3.0 30.5 1.0
CD2 A:HIS529 3.1 32.9 1.0
CG A:ASP674 3.1 33.8 1.0
CG A:ASP564 3.1 35.0 1.0
CE1 A:HIS529 3.2 35.7 1.0
CE1 A:HIS563 3.3 33.6 1.0
OD2 A:ASP674 3.4 37.3 1.0
OD1 A:ASP564 3.6 30.0 1.0
MG A:MG802 3.7 32.2 1.0
CD2 A:HIS525 4.1 38.4 1.0
CG A:HIS563 4.2 30.6 1.0
O A:HOH1006 4.2 25.0 1.0
CG A:HIS529 4.2 33.7 1.0
ND1 A:HIS529 4.3 34.7 1.0
ND1 A:HIS563 4.3 31.1 1.0
CB A:ASP564 4.3 33.5 1.0
CB A:ASP674 4.4 31.9 1.0
NE2 A:HIS525 4.5 37.5 1.0
O A:HOH963 4.5 46.0 1.0
O A:HOH931 4.5 26.1 1.0
CG2 A:VAL533 4.7 27.8 1.0
O A:ASP674 4.8 31.2 1.0
CA A:ASP674 4.9 29.3 1.0
O A:HOH1035 4.9 55.0 1.0

Zinc binding site 2 out of 4 in 5sep

Go back to Zinc Binding Sites List in 5sep
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (4-Cyclopentyl-1-Methylimidazol-2-Yl)Ethyl]-5,8-Dimethyl-[1,2, 4]Triazolo[1,5-A]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-[2- (4-Cyclopentyl-1-Methylimidazol-2-Yl)Ethyl]-5,8-Dimethyl-[1,2, 4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:35.3
occ:1.00
 O B:HOH975 2.1 27.4 1.0
OD2 B:ASP564 2.1 32.3 1.0
OD1 B:ASP674 2.1 32.6 1.0
NE2 B:HIS529 2.2 26.8 1.0
NE2 B:HIS563 2.2 25.5 1.0
O B:HOH955 2.4 43.2 1.0
CD2 B:HIS563 3.0 29.5 1.0
CD2 B:HIS529 3.0 30.2 1.0
CG B:ASP674 3.1 30.2 1.0
CG B:ASP564 3.1 27.9 1.0
CE1 B:HIS529 3.2 29.0 1.0
CE1 B:HIS563 3.3 28.9 1.0
OD2 B:ASP674 3.3 34.0 1.0
OD1 B:ASP564 3.6 31.8 1.0
MG B:MG802 3.7 29.2 1.0
CD2 B:HIS525 4.0 31.1 1.0
O B:HOH1017 4.1 25.4 1.0
CG B:HIS563 4.2 27.3 1.0
CG B:HIS529 4.2 29.1 1.0
ND1 B:HIS529 4.3 26.1 1.0
ND1 B:HIS563 4.3 29.1 1.0
CB B:ASP564 4.3 28.7 1.0
O B:HOH985 4.4 51.5 1.0
CB B:ASP674 4.4 31.3 1.0
NE2 B:HIS525 4.4 32.1 1.0
O B:HOH961 4.5 30.5 1.0
O B:HOH1055 4.5 57.7 1.0
CG2 B:VAL533 4.7 27.0 1.0
CA B:ASP674 4.8 27.5 1.0
O B:ASP674 4.9 28.1 1.0

Zinc binding site 3 out of 4 in 5sep

Go back to Zinc Binding Sites List in 5sep
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (4-Cyclopentyl-1-Methylimidazol-2-Yl)Ethyl]-5,8-Dimethyl-[1,2, 4]Triazolo[1,5-A]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-[2- (4-Cyclopentyl-1-Methylimidazol-2-Yl)Ethyl]-5,8-Dimethyl-[1,2, 4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:35.9
occ:1.00
 O C:HOH977 2.1 27.1 1.0
NE2 C:HIS529 2.1 32.8 1.0
OD2 C:ASP564 2.2 31.8 1.0
NE2 C:HIS563 2.2 32.1 1.0
OD1 C:ASP674 2.2 28.6 1.0
O C:HOH981 2.4 47.0 1.0
CD2 C:HIS563 3.0 31.1 1.0
CG C:ASP674 3.1 30.2 1.0
CD2 C:HIS529 3.1 31.9 1.0
CE1 C:HIS529 3.2 33.0 1.0
CG C:ASP564 3.2 30.1 1.0
OD2 C:ASP674 3.3 35.9 1.0
CE1 C:HIS563 3.3 32.1 1.0
OD1 C:ASP564 3.7 29.0 1.0
MG C:MG802 3.8 31.8 1.0
CD2 C:HIS525 4.1 32.8 1.0
CG C:HIS563 4.2 30.4 1.0
O C:HOH1026 4.3 29.2 1.0
CG C:HIS529 4.3 30.9 1.0
ND1 C:HIS529 4.3 30.9 1.0
ND1 C:HIS563 4.3 29.9 1.0
CB C:ASP564 4.4 27.8 1.0
NE2 C:HIS525 4.4 33.5 1.0
CB C:ASP674 4.4 32.4 1.0
O C:HOH1019 4.4 42.3 1.0
O C:HOH1039 4.5 60.0 1.0
O C:HOH953 4.5 29.6 1.0
CG2 C:VAL533 4.7 30.5 1.0
CA C:ASP674 4.8 33.7 1.0
O C:ASP674 4.9 37.1 1.0

Zinc binding site 4 out of 4 in 5sep

Go back to Zinc Binding Sites List in 5sep
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (4-Cyclopentyl-1-Methylimidazol-2-Yl)Ethyl]-5,8-Dimethyl-[1,2, 4]Triazolo[1,5-A]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-[2- (4-Cyclopentyl-1-Methylimidazol-2-Yl)Ethyl]-5,8-Dimethyl-[1,2, 4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:45.9
occ:1.00
 O D:HOH959 2.0 35.1 1.0
NE2 D:HIS529 2.2 40.5 1.0
OD2 D:ASP564 2.2 47.1 1.0
OD1 D:ASP674 2.2 44.7 1.0
NE2 D:HIS563 2.2 34.0 1.0
O D:HOH940 2.3 49.9 1.0
CD2 D:HIS563 3.0 37.1 1.0
CG D:ASP674 3.1 44.1 1.0
CD2 D:HIS529 3.2 42.8 1.0
CG D:ASP564 3.2 41.4 1.0
CE1 D:HIS529 3.2 40.6 1.0
OD2 D:ASP674 3.3 47.9 1.0
CE1 D:HIS563 3.4 40.1 1.0
OD1 D:ASP564 3.7 41.6 1.0
MG D:MG802 3.8 41.9 1.0
CD2 D:HIS525 4.1 43.1 1.0
O D:HOH970 4.2 35.9 1.0
CG D:HIS563 4.2 37.1 1.0
ND1 D:HIS529 4.3 42.9 1.0
CG D:HIS529 4.3 38.0 1.0
CB D:ASP564 4.3 41.0 1.0
ND1 D:HIS563 4.4 38.7 1.0
O D:HOH944 4.4 56.3 1.0
O D:HOH912 4.5 36.5 1.0
CB D:ASP674 4.5 44.6 1.0
NE2 D:HIS525 4.5 49.1 1.0
CG2 D:VAL533 4.7 42.0 1.0
CA D:ASP674 4.9 42.1 1.0
O D:ASP674 4.9 44.5 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 04:45:23 2024

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