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Zinc in PDB 5sfy: Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[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 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine, PDB code: 5sfy was solved by C.Joseph, A.Flohr, 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) 43.47 / 2.08
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.137, 135.137, 234.83, 90, 90, 120
R / Rfree (%) 18.2 / 22.5

Other elements in 5sfy:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[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 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine (pdb code 5sfy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine, PDB code: 5sfy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5sfy

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

b:31.5
occ:1.00
 O A:HOH966 2.1 28.9 1.0
OD2 A:ASP564 2.1 28.5 1.0
NE2 A:HIS529 2.1 26.1 1.0
NE2 A:HIS563 2.2 27.4 1.0
OD1 A:ASP674 2.2 31.3 1.0
O A:HOH974 2.2 33.1 1.0
CD2 A:HIS563 3.0 25.6 1.0
CD2 A:HIS529 3.1 25.4 1.0
CG A:ASP564 3.1 26.9 1.0
CE1 A:HIS529 3.1 26.7 1.0
CG A:ASP674 3.1 30.9 1.0
CE1 A:HIS563 3.2 26.8 1.0
OD2 A:ASP674 3.4 37.0 1.0
OD1 A:ASP564 3.5 26.2 1.0
MG A:MG802 3.8 29.3 1.0
ZN A:ZN804 4.0 49.9 0.5
O A:HOH990 4.0 27.4 1.0
CD2 A:HIS525 4.1 29.1 1.0
CG A:HIS563 4.2 26.5 1.0
ND1 A:HIS529 4.2 24.2 1.0
CG A:HIS529 4.2 24.5 1.0
ND1 A:HIS563 4.3 27.2 1.0
CB A:ASP564 4.3 26.8 1.0
NE2 A:HIS525 4.5 31.8 1.0
CB A:ASP674 4.5 26.8 1.0
O A:HOH976 4.5 42.9 1.0
O A:HOH911 4.6 24.0 1.0
CG2 A:VAL533 4.7 22.2 1.0
CA A:ASP674 4.9 26.1 1.0
O A:ASP674 5.0 27.1 1.0

Zinc binding site 2 out of 8 in 5sfy

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Zinc binding site 2 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[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 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn804

b:49.9
occ:0.50
 NE2 A:HIS525 2.1 31.8 1.0
O A:HOH974 2.1 33.1 1.0
O A:HOH990 2.2 27.4 1.0
CE1 A:HIS525 3.0 26.8 1.0
O A:HOH1002 3.0 43.6 1.0
CD2 A:HIS525 3.1 29.1 1.0
O A:HOH966 3.4 28.9 1.0
MG A:MG802 3.9 29.3 1.0
O A:HOH976 3.9 42.9 1.0
ZN A:ZN801 4.0 31.5 1.0
O A:HOH958 4.1 31.9 1.0
ND1 A:HIS525 4.1 27.1 1.0
CG A:HIS525 4.2 29.5 1.0
O A:HOH923 4.3 23.6 1.0
OD2 A:ASP564 4.4 28.5 1.0
CE2 A:TYR524 4.6 31.0 1.0
OD2 A:ASP674 4.7 37.0 1.0
OD1 A:ASP674 4.8 31.3 1.0
OD1 A:ASP564 4.9 26.2 1.0
O A:HOH935 5.0 33.8 1.0
NE2 A:HIS567 5.0 29.7 1.0

Zinc binding site 3 out of 8 in 5sfy

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

b:30.6
occ:1.00
 NE2 B:HIS563 2.1 24.4 1.0
NE2 B:HIS529 2.2 22.4 1.0
OD1 B:ASP674 2.2 32.8 1.0
OD2 B:ASP564 2.2 28.6 1.0
O B:HOH939 2.2 19.7 1.0
CD2 B:HIS529 3.0 25.0 1.0
CG B:ASP674 3.1 30.0 1.0
CD2 B:HIS563 3.1 23.6 1.0
CE1 B:HIS563 3.1 23.5 1.0
CG B:ASP564 3.2 26.2 1.0
CE1 B:HIS529 3.3 24.8 1.0
OD2 B:ASP674 3.3 32.7 1.0
OD1 B:ASP564 3.7 26.4 1.0
ZN B:ZN804 3.7 50.2 0.5
MG B:MG802 3.9 27.4 1.0
O B:HOH993 3.9 27.6 1.0
CD2 B:HIS525 4.1 23.2 1.0
ND1 B:HIS563 4.2 23.7 1.0
CG B:HIS563 4.2 23.7 1.0
CG B:HIS529 4.2 25.0 1.0
O B:HOH943 4.3 40.2 1.0
ND1 B:HIS529 4.3 22.9 1.0
O B:HOH995 4.4 39.3 1.0
CB B:ASP564 4.4 25.0 1.0
CB B:ASP674 4.5 26.5 1.0
NE2 B:HIS525 4.5 24.4 1.0
O B:HOH929 4.6 26.8 1.0
CG2 B:VAL533 4.6 20.2 1.0
CA B:ASP674 4.9 23.7 1.0
O B:ASP674 4.9 25.4 1.0

Zinc binding site 4 out of 8 in 5sfy

Go back to Zinc Binding Sites List in 5sfy
Zinc binding site 4 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[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 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn804

b:50.2
occ:0.50
 O B:HOH993 2.2 27.6 1.0
NE2 B:HIS525 2.2 24.4 1.0
O B:HOH995 2.3 39.3 1.0
CD2 B:HIS525 3.1 23.2 1.0
O B:HOH1007 3.1 42.0 1.0
CE1 B:HIS525 3.2 23.2 1.0
O B:HOH939 3.3 19.7 1.0
O B:HOH943 3.7 40.2 1.0
ZN B:ZN801 3.7 30.6 1.0
MG B:MG802 4.0 27.4 1.0
O B:HOH949 4.2 25.9 1.0
OD2 B:ASP674 4.3 32.7 1.0
CG B:HIS525 4.3 22.4 1.0
ND1 B:HIS525 4.3 24.7 1.0
OD2 B:ASP564 4.4 28.6 1.0
O B:HOH903 4.4 22.3 1.0
OD1 B:ASP674 4.4 32.8 1.0
CE2 B:TYR524 4.5 33.3 1.0
NE2 B:HIS529 4.8 22.4 1.0
CG B:ASP674 4.8 30.0 1.0
O B:HOH980 4.8 34.3 1.0
OD1 B:ASP564 4.9 26.4 1.0

Zinc binding site 5 out of 8 in 5sfy

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Zinc binding site 5 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[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 5 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:31.1
occ:1.00
 O C:HOH940 2.1 22.2 1.0
NE2 C:HIS529 2.1 24.8 1.0
OD1 C:ASP674 2.2 27.3 1.0
O C:HOH967 2.2 37.5 1.0
OD2 C:ASP564 2.2 28.4 1.0
NE2 C:HIS563 2.3 24.7 1.0
CG C:ASP674 3.1 28.4 1.0
CD2 C:HIS529 3.1 23.9 1.0
CD2 C:HIS563 3.1 24.0 1.0
CE1 C:HIS529 3.2 26.5 1.0
CG C:ASP564 3.2 26.2 1.0
OD2 C:ASP674 3.3 31.5 1.0
CE1 C:HIS563 3.4 23.6 1.0
OD1 C:ASP564 3.6 27.0 1.0
MG C:MG802 3.7 25.3 1.0
ZN C:ZN804 4.0 46.4 0.5
CD2 C:HIS525 4.0 29.7 1.0
O C:HOH982 4.1 23.6 1.0
O C:HOH985 4.2 38.7 1.0
ND1 C:HIS529 4.3 24.3 1.0
CG C:HIS529 4.3 24.1 1.0
CG C:HIS563 4.3 24.9 1.0
CB C:ASP564 4.3 24.8 1.0
NE2 C:HIS525 4.4 30.4 1.0
ND1 C:HIS563 4.4 26.1 1.0
CB C:ASP674 4.5 25.5 1.0
O C:HOH916 4.6 22.3 1.0
CG2 C:VAL533 4.8 22.4 1.0
CA C:ASP674 4.9 26.8 1.0
O C:ASP674 4.9 26.9 1.0

Zinc binding site 6 out of 8 in 5sfy

Go back to Zinc Binding Sites List in 5sfy
Zinc binding site 6 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[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 6 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn804

b:46.4
occ:0.50
 O C:HOH967 2.1 37.5 1.0
NE2 C:HIS525 2.1 30.4 1.0
O C:HOH982 2.2 23.6 1.0
O C:HOH1001 3.0 50.2 1.0
CE1 C:HIS525 3.1 30.2 1.0
CD2 C:HIS525 3.1 29.7 1.0
O C:HOH940 3.3 22.2 1.0
O C:HOH950 3.8 32.7 1.0
O C:HOH985 3.8 38.7 1.0
MG C:MG802 3.8 25.3 1.0
ZN C:ZN801 4.0 31.1 1.0
ND1 C:HIS525 4.2 31.8 1.0
CG C:HIS525 4.2 30.6 1.0
O C:HOH918 4.3 26.0 1.0
OD2 C:ASP564 4.4 28.4 1.0
OD2 C:ASP674 4.5 31.5 1.0
NE2 C:HIS567 4.7 32.3 1.0
OD1 C:ASP564 4.7 27.0 1.0
O C:HOH976 4.7 34.5 1.0
OD1 C:ASP674 4.8 27.3 1.0
O C:HOH981 4.8 25.7 1.0
CE2 C:TYR524 4.8 30.3 1.0
CG C:ASP564 5.0 26.2 1.0

Zinc binding site 7 out of 8 in 5sfy

Go back to Zinc Binding Sites List in 5sfy
Zinc binding site 7 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[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 7 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:36.7
occ:1.00
 O D:HOH931 2.0 27.4 1.0
O D:HOH952 2.1 42.8 1.0
NE2 D:HIS563 2.2 24.9 1.0
OD1 D:ASP674 2.2 35.1 1.0
OD2 D:ASP564 2.2 35.7 1.0
NE2 D:HIS529 2.3 31.1 1.0
CD2 D:HIS563 3.0 28.0 1.0
CG D:ASP674 3.1 33.2 1.0
CG D:ASP564 3.2 33.0 1.0
CD2 D:HIS529 3.2 34.9 1.0
OD2 D:ASP674 3.3 37.0 1.0
CE1 D:HIS563 3.3 29.8 1.0
CE1 D:HIS529 3.3 30.8 1.0
OD1 D:ASP564 3.6 32.2 1.0
MG D:MG802 3.8 37.8 1.0
ZN D:ZN804 3.9 55.6 0.5
O D:HOH929 4.0 38.8 1.0
CD2 D:HIS525 4.1 35.1 1.0
CG D:HIS563 4.2 26.8 1.0
O D:HOH927 4.2 45.0 1.0
ND1 D:HIS563 4.3 27.5 1.0
CB D:ASP564 4.4 31.5 1.0
CG D:HIS529 4.4 33.6 1.0
ND1 D:HIS529 4.4 31.4 1.0
CB D:ASP674 4.5 33.2 1.0
NE2 D:HIS525 4.5 43.5 1.0
O D:HOH908 4.6 32.5 1.0
CG2 D:VAL533 4.7 32.2 1.0
O D:ASP674 4.8 36.0 1.0
CA D:ASP674 4.9 32.1 1.0

Zinc binding site 8 out of 8 in 5sfy

Go back to Zinc Binding Sites List in 5sfy
Zinc binding site 8 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[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 8 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn804

b:55.6
occ:0.50
 O D:HOH952 2.0 42.8 1.0
NE2 D:HIS525 2.1 43.5 1.0
O D:HOH929 2.3 38.8 1.0
CE1 D:HIS525 3.1 39.2 1.0
CD2 D:HIS525 3.2 35.1 1.0
O D:HOH931 3.6 27.4 1.0
O D:HOH970 3.6 49.4 1.0
O D:HOH927 3.7 45.0 1.0
ZN D:ZN801 3.9 36.7 1.0
O D:HOH924 4.0 42.3 1.0
MG D:MG802 4.0 37.8 1.0
ND1 D:HIS525 4.2 37.0 1.0
CG D:HIS525 4.3 35.0 1.0
O D:HOH911 4.4 30.5 1.0
OD2 D:ASP564 4.5 35.7 1.0
OD2 D:ASP674 4.6 37.0 1.0
CE2 D:TYR524 4.6 39.0 1.0
OD1 D:ASP674 4.7 35.1 1.0
O D:HOH961 4.7 39.7 1.0
OD1 D:ASP564 4.9 32.2 1.0
NE2 D:HIS529 4.9 31.1 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 05:04:36 2024

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