Zinc in PDB 5seq: Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,6,8- Trimethyl-2-[2-(2-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 5,6,8- Trimethyl-2-[2-(2-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 5,6,8- Trimethyl-2-[2-(2-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 5,6,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine, PDB code: 5seq was solved by C.Joseph, C.Lerner, 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) 43.68 / 2.18
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.275, 135.275, 235.377, 90, 90, 120
R / Rfree (%) 17.2 / 22.9

Other elements in 5seq:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,6,8- Trimethyl-2-[2-(2-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 5,6,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine (pdb code 5seq). 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 5,6,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine, PDB code: 5seq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5seq

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,6,8- Trimethyl-2-[2-(2-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 5,6,8- Trimethyl-2-[2-(2-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:Zn801

b:41.0
occ:1.00
 NE2 A:HIS529 2.2 38.0 1.0
O A:HOH950 2.2 32.8 1.0
NE2 A:HIS563 2.2 32.4 1.0
O A:HOH968 2.2 44.3 1.0
OD2 A:ASP564 2.2 39.0 1.0
OD1 A:ASP674 2.3 39.5 1.0
CD2 A:HIS563 3.0 33.8 1.0
CG A:ASP674 3.1 38.9 1.0
CE1 A:HIS529 3.1 38.3 1.0
CG A:ASP564 3.2 37.0 1.0
CD2 A:HIS529 3.2 34.7 1.0
OD2 A:ASP674 3.2 40.5 1.0
CE1 A:HIS563 3.3 37.1 1.0
OD1 A:ASP564 3.6 34.9 1.0
MG A:MG802 3.8 36.9 1.0
O A:HOH986 4.1 32.7 1.0
CD2 A:HIS525 4.1 36.8 1.0
CG A:HIS563 4.2 35.3 1.0
ND1 A:HIS529 4.2 36.6 1.0
ND1 A:HIS563 4.3 32.9 1.0
CG A:HIS529 4.3 36.2 1.0
CB A:ASP564 4.3 32.8 1.0
CB A:ASP674 4.4 41.2 1.0
NE2 A:HIS525 4.5 36.6 1.0
O A:HOH919 4.5 28.8 1.0
CG2 A:VAL533 4.7 36.2 1.0
CA A:ASP674 4.9 37.3 1.0
O A:ASP674 5.0 38.2 1.0

Zinc binding site 2 out of 4 in 5seq

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,6,8- Trimethyl-2-[2-(2-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 5,6,8- Trimethyl-2-[2-(2-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:Zn801

b:39.4
occ:1.00
 NE2 B:HIS563 2.1 32.5 1.0
O B:HOH957 2.1 30.2 1.0
NE2 B:HIS529 2.2 33.6 1.0
OD2 B:ASP564 2.2 38.1 1.0
OD1 B:ASP674 2.2 34.1 1.0
O B:HOH942 2.5 47.7 1.0
CD2 B:HIS563 3.0 35.1 1.0
CG B:ASP674 3.1 33.0 1.0
CD2 B:HIS529 3.1 36.3 1.0
CE1 B:HIS563 3.1 30.7 1.0
CG B:ASP564 3.2 35.7 1.0
CE1 B:HIS529 3.2 33.8 1.0
OD2 B:ASP674 3.2 36.9 1.0
OD1 B:ASP564 3.6 33.8 1.0
MG B:MG802 3.8 35.1 1.0
O B:HOH979 4.0 29.8 1.0
CD2 B:HIS525 4.1 35.7 1.0
CG B:HIS563 4.2 31.8 1.0
ND1 B:HIS563 4.2 29.5 1.0
CG B:HIS529 4.3 33.2 1.0
ND1 B:HIS529 4.3 31.9 1.0
CB B:ASP564 4.4 35.6 1.0
CB B:ASP674 4.4 31.9 1.0
NE2 B:HIS525 4.5 38.8 1.0
O B:HOH921 4.6 34.5 1.0
CG2 B:VAL533 4.7 32.3 1.0
CA B:ASP674 4.8 29.4 1.0
O B:ASP674 4.9 36.8 1.0

Zinc binding site 3 out of 4 in 5seq

Go back to Zinc Binding Sites List in 5seq
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,6,8- Trimethyl-2-[2-(2-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 5,6,8- Trimethyl-2-[2-(2-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:Zn801

b:40.0
occ:1.00
 O C:HOH930 2.0 31.4 1.0
NE2 C:HIS529 2.1 37.8 1.0
OD2 C:ASP564 2.2 34.9 1.0
NE2 C:HIS563 2.3 30.8 1.0
OD1 C:ASP674 2.3 33.2 1.0
O C:HOH959 2.4 52.4 1.0
CD2 C:HIS563 3.0 31.0 1.0
CG C:ASP674 3.1 33.2 1.0
CD2 C:HIS529 3.1 35.3 1.0
CE1 C:HIS529 3.1 38.2 1.0
CG C:ASP564 3.2 34.8 1.0
OD2 C:ASP674 3.2 36.9 1.0
CE1 C:HIS563 3.4 33.1 1.0
OD1 C:ASP564 3.6 34.5 1.0
MG C:MG802 3.8 33.8 1.0
CD2 C:HIS525 4.2 35.7 1.0
O C:HOH988 4.2 28.8 1.0
ND1 C:HIS529 4.2 34.4 1.0
CG C:HIS529 4.2 31.9 1.0
CG C:HIS563 4.3 31.3 1.0
CB C:ASP564 4.4 31.5 1.0
ND1 C:HIS563 4.4 30.4 1.0
CB C:ASP674 4.5 36.8 1.0
NE2 C:HIS525 4.5 40.7 1.0
O C:HOH932 4.5 33.5 1.0
CG2 C:VAL533 4.8 36.7 1.0
O C:HOH976 4.8 58.0 1.0
CA C:ASP674 4.8 36.1 1.0
O C:ASP674 5.0 36.5 1.0

Zinc binding site 4 out of 4 in 5seq

Go back to Zinc Binding Sites List in 5seq
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,6,8- Trimethyl-2-[2-(2-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 5,6,8- Trimethyl-2-[2-(2-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:Zn801

b:55.8
occ:1.00
 O D:HOH920 1.9 41.6 1.0
NE2 D:HIS563 2.2 45.0 1.0
OD2 D:ASP564 2.2 55.9 1.0
NE2 D:HIS529 2.2 46.9 1.0
O D:HOH926 2.3 56.0 1.0
OD1 D:ASP674 2.4 47.1 1.0
CD2 D:HIS563 3.0 46.9 1.0
CD2 D:HIS529 3.1 59.4 1.0
CE1 D:HIS529 3.2 51.2 1.0
CG D:ASP564 3.2 50.7 1.0
CG D:ASP674 3.2 50.8 1.0
CE1 D:HIS563 3.3 51.5 1.0
OD2 D:ASP674 3.4 55.4 1.0
OD1 D:ASP564 3.8 50.9 1.0
MG D:MG802 3.8 48.9 1.0
CD2 D:HIS525 4.1 55.1 1.0
O D:HOH931 4.2 46.4 1.0
CG D:HIS563 4.2 49.2 1.0
ND1 D:HIS529 4.3 54.7 1.0
CG D:HIS529 4.3 50.9 1.0
ND1 D:HIS563 4.3 49.0 1.0
CB D:ASP564 4.3 49.2 1.0
NE2 D:HIS525 4.5 63.5 1.0
CB D:ASP674 4.6 56.3 1.0
CG2 D:VAL533 4.6 50.6 1.0
O D:HOH911 4.7 45.9 1.0
O D:ASP674 4.9 59.3 1.0
CA D:ASP674 4.9 56.7 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 04:46:48 2024

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