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Zinc in PDB 5sef: Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine, PDB code: 5sef 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) 43.82 / 2.29
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.272, 135.272, 236.018, 90, 90, 120
R / Rfree (%) 17.2 / 23.2

Other elements in 5sef:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine 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 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine (pdb code 5sef). 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 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine, PDB code: 5sef:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sef

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine


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 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:46.8
occ:1.00
 OD2 A:ASP564 2.1 43.5 1.0
OD1 A:ASP674 2.1 44.2 1.0
NE2 A:HIS529 2.1 47.2 1.0
O A:HOH953 2.1 42.7 1.0
O A:HOH948 2.2 36.6 1.0
NE2 A:HIS563 2.2 36.4 1.0
CG A:ASP674 3.0 40.0 1.0
CD2 A:HIS563 3.0 41.6 1.0
CE1 A:HIS529 3.1 47.4 1.0
CG A:ASP564 3.1 37.1 1.0
CD2 A:HIS529 3.1 42.8 1.0
OD2 A:ASP674 3.3 43.5 1.0
CE1 A:HIS563 3.3 42.9 1.0
OD1 A:ASP564 3.6 39.3 1.0
MG A:MG803 3.8 38.5 1.0
CD2 A:HIS525 4.2 41.4 1.0
O A:HOH959 4.2 31.0 1.0
ND1 A:HIS529 4.2 45.4 1.0
CG A:HIS563 4.2 40.1 1.0
CG A:HIS529 4.3 42.5 1.0
CB A:ASP564 4.3 33.1 1.0
ND1 A:HIS563 4.4 37.0 1.0
CB A:ASP674 4.4 43.2 1.0
NE2 A:HIS525 4.5 43.0 1.0
O A:HOH909 4.6 30.2 1.0
CG2 A:VAL533 4.8 37.6 1.0
CA A:ASP674 4.8 40.5 1.0
O A:HOH935 5.0 35.3 1.0
O A:ASP674 5.0 43.4 1.0

Zinc binding site 2 out of 4 in 5sef

Go back to Zinc Binding Sites List in 5sef
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine


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 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:44.2
occ:1.00
 OD2 B:ASP564 2.1 40.6 1.0
OD1 B:ASP674 2.1 42.2 1.0
O B:HOH943 2.1 29.9 1.0
NE2 B:HIS563 2.2 36.1 1.0
NE2 B:HIS529 2.2 36.2 1.0
O B:HOH922 2.5 43.7 1.0
CG B:ASP674 3.0 38.2 1.0
CD2 B:HIS563 3.0 39.5 1.0
CG B:ASP564 3.1 38.3 1.0
CD2 B:HIS529 3.1 38.7 1.0
CE1 B:HIS529 3.2 39.3 1.0
CE1 B:HIS563 3.2 37.6 1.0
OD2 B:ASP674 3.3 38.9 1.0
OD1 B:ASP564 3.6 35.7 1.0
MG B:MG803 3.8 36.4 1.0
O B:HOH944 3.9 29.7 1.0
CD2 B:HIS525 4.1 42.5 1.0
CG B:HIS563 4.2 35.7 1.0
ND1 B:HIS563 4.3 38.9 1.0
CG B:HIS529 4.3 40.9 1.0
ND1 B:HIS529 4.3 41.6 1.0
CB B:ASP564 4.3 36.1 1.0
CB B:ASP674 4.4 38.6 1.0
NE2 B:HIS525 4.5 45.2 1.0
O B:HOH925 4.7 37.1 1.0
CG2 B:VAL533 4.7 36.1 1.0
CA B:ASP674 4.8 36.1 1.0
O B:ASP674 4.9 41.9 1.0

Zinc binding site 3 out of 4 in 5sef

Go back to Zinc Binding Sites List in 5sef
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine


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 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn802

b:44.3
occ:1.00
 O C:HOH917 1.9 32.3 1.0
OD2 C:ASP564 2.1 44.2 1.0
NE2 C:HIS529 2.2 39.5 1.0
O C:HOH954 2.2 45.7 1.0
NE2 C:HIS563 2.2 34.9 1.0
OD1 C:ASP674 2.3 44.2 1.0
CD2 C:HIS563 3.1 38.3 1.0
CG C:ASP674 3.1 36.4 1.0
CD2 C:HIS529 3.1 38.3 1.0
CG C:ASP564 3.1 36.8 1.0
CE1 C:HIS529 3.2 39.2 1.0
OD2 C:ASP674 3.2 40.9 1.0
CE1 C:HIS563 3.2 36.6 1.0
OD1 C:ASP564 3.6 40.1 1.0
MG C:MG803 3.7 38.2 1.0
CD2 C:HIS525 4.1 43.6 1.0
CG C:HIS563 4.2 34.9 1.0
CG C:HIS529 4.3 36.0 1.0
O C:HOH964 4.3 34.4 1.0
ND1 C:HIS529 4.3 41.4 1.0
CB C:ASP564 4.3 35.1 1.0
ND1 C:HIS563 4.3 34.9 1.0
NE2 C:HIS525 4.4 46.6 1.0
CB C:ASP674 4.5 38.7 1.0
O C:HOH929 4.6 39.9 1.0
CG2 C:VAL533 4.7 41.2 1.0
CA C:ASP674 4.8 41.3 1.0
O C:ASP674 5.0 42.4 1.0

Zinc binding site 4 out of 4 in 5sef

Go back to Zinc Binding Sites List in 5sef
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine


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 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn802

b:62.2
occ:1.00
 O D:HOH915 2.0 45.1 1.0
NE2 D:HIS563 2.1 50.9 1.0
OD2 D:ASP564 2.2 69.1 1.0
NE2 D:HIS529 2.3 52.3 1.0
OD1 D:ASP674 2.3 59.9 1.0
O D:HOH911 2.4 56.1 1.0
CD2 D:HIS563 3.0 61.8 1.0
CD2 D:HIS529 3.1 61.4 1.0
CG D:ASP564 3.2 54.6 1.0
CE1 D:HIS563 3.2 56.4 1.0
CG D:ASP674 3.3 56.9 1.0
CE1 D:HIS529 3.4 57.1 1.0
OD2 D:ASP674 3.7 72.8 1.0
MG D:MG803 3.8 54.2 1.0
OD1 D:ASP564 3.8 57.6 1.0
O D:HOH904 4.1 48.4 1.0
CD2 D:HIS525 4.2 66.3 1.0
CG D:HIS563 4.2 61.1 1.0
CB D:ASP564 4.2 56.0 1.0
ND1 D:HIS563 4.3 56.3 1.0
CG D:HIS529 4.3 49.6 1.0
ND1 D:HIS529 4.4 63.5 1.0
NE2 D:HIS525 4.6 64.2 1.0
CB D:ASP674 4.6 64.1 1.0
O D:HOH906 4.6 57.9 1.0
CG2 D:VAL533 4.7 58.7 1.0
O D:ASP674 4.9 62.3 1.0
CA D:ASP674 4.9 63.4 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 04:39:33 2024

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