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Zinc in PDB 5sej: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine, PDB code: 5sej 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) 43.62 / 2.44
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.506, 135.506, 234.911, 90, 90, 120
R / Rfree (%) 17.4 / 24.3

Other elements in 5sej:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine (pdb code 5sej). 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 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine, PDB code: 5sej:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sej

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine


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 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:49.6
occ:1.00
 O A:HOH924 2.0 43.4 1.0
NE2 A:HIS529 2.1 46.2 1.0
OD1 A:ASP674 2.1 52.3 1.0
OD2 A:ASP564 2.1 40.2 1.0
NE2 A:HIS563 2.2 38.2 1.0
O A:HOH915 2.4 39.3 1.0
CE1 A:HIS529 2.9 42.8 1.0
CG A:ASP674 3.0 47.1 1.0
CD2 A:HIS563 3.1 38.6 1.0
CD2 A:HIS529 3.2 44.5 1.0
CG A:ASP564 3.2 34.5 1.0
CE1 A:HIS563 3.2 40.4 1.0
OD2 A:ASP674 3.3 41.9 1.0
OD1 A:ASP564 3.7 37.6 1.0
MG A:MG802 3.9 44.8 1.0
CD2 A:HIS525 4.0 46.2 1.0
O A:HOH948 4.1 28.3 1.0
ND1 A:HIS529 4.1 46.3 1.0
O A:HOH936 4.2 47.3 1.0
CG A:HIS529 4.2 41.1 1.0
CG A:HIS563 4.3 36.6 1.0
NE2 A:HIS525 4.3 45.1 1.0
ND1 A:HIS563 4.3 37.2 1.0
CB A:ASP564 4.4 32.5 1.0
CB A:ASP674 4.4 40.8 1.0
O A:HOH905 4.6 32.5 1.0
CG2 A:VAL533 4.7 33.8 1.0
O A:ASP674 4.8 43.4 1.0
CA A:ASP674 4.9 42.8 1.0
O A:HOH904 5.0 40.9 1.0

Zinc binding site 2 out of 4 in 5sej

Go back to Zinc Binding Sites List in 5sej
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine


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 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:42.4
occ:1.00
 NE2 B:HIS529 2.1 32.2 1.0
O B:HOH935 2.1 29.4 1.0
NE2 B:HIS563 2.1 31.5 1.0
OD2 B:ASP564 2.2 41.7 1.0
OD1 B:ASP674 2.3 37.1 1.0
O B:HOH914 2.6 36.7 1.0
CD2 B:HIS529 3.0 32.9 1.0
CD2 B:HIS563 3.0 34.9 1.0
CG B:ASP674 3.1 37.8 1.0
CE1 B:HIS529 3.2 34.1 1.0
CG B:ASP564 3.2 39.2 1.0
CE1 B:HIS563 3.2 32.8 1.0
OD2 B:ASP674 3.4 41.6 1.0
OD1 B:ASP564 3.6 35.9 1.0
MG B:MG802 3.8 32.1 1.0
O B:HOH949 3.9 27.0 1.0
CG B:HIS529 4.1 34.1 1.0
O B:HOH928 4.2 43.8 1.0
CD2 B:HIS525 4.2 41.5 1.0
ND1 B:HIS529 4.2 34.8 1.0
CG B:HIS563 4.2 33.0 1.0
ND1 B:HIS563 4.3 33.6 1.0
CB B:ASP564 4.4 35.7 1.0
CB B:ASP674 4.4 40.1 1.0
NE2 B:HIS525 4.5 37.9 1.0
CG2 B:VAL533 4.6 31.0 1.0
CA B:ASP674 4.8 35.9 1.0
O B:ASP674 4.9 40.3 1.0
O B:HOH920 4.9 28.4 1.0

Zinc binding site 3 out of 4 in 5sej

Go back to Zinc Binding Sites List in 5sej
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine


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 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:45.2
occ:1.00
 OD2 C:ASP564 2.1 40.3 1.0
O C:HOH919 2.1 35.0 1.0
OD1 C:ASP674 2.1 41.2 1.0
NE2 C:HIS529 2.2 35.0 1.0
NE2 C:HIS563 2.2 38.2 1.0
CG C:ASP674 3.0 37.8 1.0
CD2 C:HIS563 3.1 35.5 1.0
CG C:ASP564 3.2 33.5 1.0
CD2 C:HIS529 3.2 36.4 1.0
CE1 C:HIS529 3.2 36.6 1.0
OD2 C:ASP674 3.2 38.1 1.0
CE1 C:HIS563 3.3 37.4 1.0
MG C:MG802 3.6 36.4 1.0
OD1 C:ASP564 3.7 34.2 1.0
CD2 C:HIS525 4.1 42.0 1.0
O C:HOH952 4.2 39.6 1.0
O C:HOH972 4.2 47.8 1.0
CG C:HIS563 4.3 36.3 1.0
ND1 C:HIS529 4.3 31.9 1.0
CG C:HIS529 4.3 33.0 1.0
ND1 C:HIS563 4.3 36.1 1.0
O C:HOH929 4.3 50.2 1.0
CB C:ASP564 4.4 35.2 1.0
NE2 C:HIS525 4.4 48.2 1.0
CB C:ASP674 4.4 36.8 1.0
O C:HOH933 4.5 30.5 1.0
CA C:ASP674 4.9 39.8 1.0
CG2 C:VAL533 4.9 36.8 1.0
O C:HOH911 4.9 28.1 1.0
O C:ASP674 4.9 43.4 1.0

Zinc binding site 4 out of 4 in 5sej

Go back to Zinc Binding Sites List in 5sej
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine


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 6- Chloro-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-[1, 2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:63.7
occ:1.00
 NE2 D:HIS563 2.2 49.2 1.0
O D:HOH925 2.2 47.4 1.0
OD2 D:ASP564 2.2 71.3 1.0
O D:HOH916 2.3 45.0 1.0
NE2 D:HIS529 2.3 53.0 1.0
OD1 D:ASP674 2.4 63.6 1.0
CD2 D:HIS563 2.9 57.8 1.0
CD2 D:HIS529 3.0 59.4 1.0
CG D:ASP564 3.2 57.4 1.0
CE1 D:HIS563 3.3 51.9 1.0
CG D:ASP674 3.3 55.9 1.0
CE1 D:HIS529 3.5 61.0 1.0
OD2 D:ASP674 3.6 61.7 1.0
OD1 D:ASP564 3.8 57.2 1.0
MG D:MG802 3.8 56.5 1.0
O D:HOH912 3.9 48.6 1.0
CG D:HIS563 4.1 56.6 1.0
CD2 D:HIS525 4.1 62.9 1.0
CB D:ASP564 4.2 54.3 1.0
ND1 D:HIS563 4.3 51.0 1.0
CG D:HIS529 4.3 60.9 1.0
ND1 D:HIS529 4.5 64.1 1.0
NE2 D:HIS525 4.5 59.1 1.0
O D:HOH901 4.6 58.9 1.0
CB D:ASP674 4.6 69.8 1.0
CG2 D:VAL533 4.8 61.6 1.0
O D:ASP674 4.9 77.1 1.0
CA D:ASP674 5.0 65.3 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 04:42:28 2024

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