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Zinc in PDB 5sft: Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(1-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(1-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [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-[2-(1-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [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-[2-(1-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine, PDB code: 5sft 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) 43.70 / 2.32
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.113, 135.113, 235.547, 90, 90, 120
R / Rfree (%) 17.6 / 22.8

Other elements in 5sft:

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

Zinc binding site 1 out of 4 in 5sft

Go back to Zinc Binding Sites List in 5sft
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(1-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [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-[2-(1-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:43.4
occ:1.00
 O A:HOH941 2.1 29.2 1.0
OD2 A:ASP564 2.1 45.8 1.0
NE2 A:HIS563 2.1 33.4 1.0
NE2 A:HIS529 2.2 38.4 1.0
OD1 A:ASP674 2.2 43.5 1.0
O A:HOH948 2.5 45.1 1.0
CD2 A:HIS563 3.0 34.1 1.0
CG A:ASP674 3.0 42.0 1.0
CG A:ASP564 3.1 40.9 1.0
CD2 A:HIS529 3.1 38.3 1.0
CE1 A:HIS529 3.2 39.3 1.0
OD2 A:ASP674 3.2 41.9 1.0
CE1 A:HIS563 3.2 39.7 1.0
OD1 A:ASP564 3.6 38.2 1.0
MG A:MG803 3.7 36.2 1.0
CD2 A:HIS525 4.1 44.2 1.0
O A:HOH946 4.1 34.4 1.0
CG A:HIS563 4.2 34.8 1.0
ND1 A:HIS529 4.3 40.5 1.0
ND1 A:HIS563 4.3 32.9 1.0
CB A:ASP564 4.3 38.3 1.0
CG A:HIS529 4.3 35.9 1.0
O A:HOH902 4.4 26.4 1.0
CB A:ASP674 4.4 41.5 1.0
NE2 A:HIS525 4.5 43.6 1.0
O A:HOH951 4.5 51.8 1.0
CG2 A:VAL533 4.8 32.9 1.0
CA A:ASP674 4.9 37.1 1.0

Zinc binding site 2 out of 4 in 5sft

Go back to Zinc Binding Sites List in 5sft
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(1-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [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-[2-(1-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:41.8
occ:1.00
 NE2 B:HIS563 2.0 35.7 1.0
OD2 B:ASP564 2.1 41.7 1.0
NE2 B:HIS529 2.1 33.4 1.0
O B:HOH923 2.1 28.3 1.0
OD1 B:ASP674 2.2 38.5 1.0
O B:HOH928 2.5 47.1 1.0
CD2 B:HIS563 3.0 36.3 1.0
CE1 B:HIS563 3.0 37.6 1.0
CD2 B:HIS529 3.1 32.9 1.0
CG B:ASP564 3.1 37.6 1.0
CG B:ASP674 3.1 37.6 1.0
CE1 B:HIS529 3.1 31.3 1.0
OD2 B:ASP674 3.4 38.1 1.0
OD1 B:ASP564 3.5 39.1 1.0
MG B:MG803 3.9 34.4 1.0
O B:HOH930 4.0 29.7 1.0
CD2 B:HIS525 4.1 40.0 1.0
ND1 B:HIS563 4.1 36.6 1.0
CG B:HIS563 4.1 33.9 1.0
ND1 B:HIS529 4.2 35.6 1.0
CG B:HIS529 4.2 33.4 1.0
CB B:ASP564 4.4 35.9 1.0
O B:HOH944 4.5 50.4 1.0
CB B:ASP674 4.5 37.7 1.0
NE2 B:HIS525 4.5 38.7 1.0
O B:HOH911 4.5 35.2 1.0
CG2 B:VAL533 4.7 32.4 1.0
CA B:ASP674 4.8 35.2 1.0
O B:ASP674 4.9 42.4 1.0

Zinc binding site 3 out of 4 in 5sft

Go back to Zinc Binding Sites List in 5sft
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(1-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [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-[2-(1-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn802

b:44.1
occ:1.00
 OD2 C:ASP564 2.1 42.9 1.0
O C:HOH911 2.1 28.0 1.0
NE2 C:HIS529 2.1 36.9 1.0
OD1 C:ASP674 2.2 38.1 1.0
NE2 C:HIS563 2.2 35.5 1.0
O C:HOH931 2.6 52.6 1.0
CD2 C:HIS563 3.0 35.2 1.0
CD2 C:HIS529 3.0 34.7 1.0
CG C:ASP674 3.1 37.0 1.0
CG C:ASP564 3.1 36.1 1.0
CE1 C:HIS529 3.1 36.6 1.0
OD2 C:ASP674 3.3 39.0 1.0
CE1 C:HIS563 3.4 37.2 1.0
OD1 C:ASP564 3.6 39.3 1.0
MG C:MG803 3.7 34.7 1.0
CD2 C:HIS525 4.0 41.9 1.0
O C:HOH950 4.1 33.4 1.0
CG C:HIS529 4.2 34.0 1.0
ND1 C:HIS529 4.2 37.1 1.0
CG C:HIS563 4.3 35.3 1.0
NE2 C:HIS525 4.3 43.9 1.0
CB C:ASP564 4.4 33.8 1.0
ND1 C:HIS563 4.4 34.6 1.0
O C:HOH909 4.5 32.8 1.0
CB C:ASP674 4.5 38.1 1.0
O C:HOH947 4.6 50.0 1.0
O C:HOH972 4.7 55.7 1.0
CG2 C:VAL533 4.8 36.9 1.0
CA C:ASP674 4.9 37.1 1.0
O C:ASP674 5.0 39.1 1.0

Zinc binding site 4 out of 4 in 5sft

Go back to Zinc Binding Sites List in 5sft
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(1-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [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-[2-(1-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn802

b:56.5
occ:1.00
 NE2 D:HIS563 2.1 48.2 1.0
O D:HOH911 2.1 40.1 1.0
OD2 D:ASP564 2.2 66.9 1.0
NE2 D:HIS529 2.2 50.2 1.0
OD1 D:ASP674 2.3 53.7 1.0
O D:HOH904 2.5 47.6 1.0
CD2 D:HIS563 3.1 49.9 1.0
CE1 D:HIS563 3.1 50.2 1.0
CD2 D:HIS529 3.1 54.9 1.0
CG D:ASP674 3.2 49.2 1.0
CG D:ASP564 3.2 53.8 1.0
CE1 D:HIS529 3.3 48.2 1.0
OD2 D:ASP674 3.4 59.2 1.0
MG D:MG803 3.8 51.4 1.0
OD1 D:ASP564 3.9 55.5 1.0
CD2 D:HIS525 4.1 55.4 1.0
O D:HOH913 4.2 42.3 1.0
CG D:HIS563 4.2 52.0 1.0
ND1 D:HIS563 4.2 47.2 1.0
CB D:ASP564 4.3 54.1 1.0
CG D:HIS529 4.3 51.4 1.0
ND1 D:HIS529 4.3 49.5 1.0
CB D:ASP674 4.5 53.9 1.0
NE2 D:HIS525 4.5 56.9 1.0
O D:HOH903 4.5 45.1 1.0
CG2 D:VAL533 4.7 49.6 1.0
CA D:ASP674 4.8 55.0 1.0
O D:ASP674 4.8 62.9 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 05:02:04 2024

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