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

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

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-6- (Trifluoromethyl)-[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 2-[2- (2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-6- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-A]Pyridine, PDB code: 5seu 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) 43.49 / 2.09
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.19, 135.19, 235.047, 90, 90, 120
R / Rfree (%) 18.3 / 23.8

Other elements in 5seu:

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

Fluorine (F) 18 atoms
Magnesium (Mg) 4 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 5seu

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-6- (Trifluoromethyl)-[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 2-[2- (2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-6- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:37.0
occ:1.00
 O A:HOH964 2.0 35.8 1.0
NE2 A:HIS529 2.1 34.6 1.0
O A:HOH970 2.2 33.8 1.0
NE2 A:HIS563 2.2 30.1 1.0
OD1 A:ASP674 2.2 37.8 1.0
OD2 A:ASP564 2.3 32.3 1.0
CD2 A:HIS563 3.0 32.9 1.0
CG A:ASP674 3.1 33.2 1.0
CD2 A:HIS529 3.1 31.1 1.0
CG A:ASP564 3.1 34.0 1.0
CE1 A:HIS529 3.1 33.5 1.0
CE1 A:HIS563 3.3 32.5 1.0
OD2 A:ASP674 3.4 39.8 1.0
OD1 A:ASP564 3.5 30.2 1.0
MG A:MG802 3.7 33.7 1.0
CD2 A:HIS525 4.1 33.6 1.0
O A:HOH966 4.1 25.1 1.0
O A:HOH937 4.1 39.3 1.0
CG A:HIS563 4.2 30.7 1.0
ND1 A:HIS529 4.3 31.0 1.0
CG A:HIS529 4.3 30.3 1.0
ND1 A:HIS563 4.3 27.8 1.0
NE2 A:HIS525 4.3 38.4 1.0
CB A:ASP564 4.3 28.8 1.0
CB A:ASP674 4.5 37.3 1.0
O A:HOH917 4.5 25.3 1.0
CG2 A:VAL533 4.8 27.2 1.0
CA A:ASP674 4.9 32.2 1.0
O A:ASP674 5.0 34.2 1.0

Zinc binding site 2 out of 4 in 5seu

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-6- (Trifluoromethyl)-[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 2-[2- (2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-6- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:34.8
occ:1.00
 O B:HOH947 2.1 28.1 1.0
NE2 B:HIS563 2.1 27.2 1.0
NE2 B:HIS529 2.2 28.0 1.0
OD1 B:ASP674 2.2 29.0 1.0
OD2 B:ASP564 2.2 33.5 1.0
O B:HOH961 2.3 38.4 1.0
CD2 B:HIS563 3.0 28.3 1.0
CD2 B:HIS529 3.1 31.2 1.0
CG B:ASP674 3.1 33.2 1.0
CE1 B:HIS563 3.1 32.0 1.0
CG B:ASP564 3.1 27.8 1.0
CE1 B:HIS529 3.2 31.4 1.0
OD2 B:ASP674 3.3 32.1 1.0
OD1 B:ASP564 3.5 31.4 1.0
MG B:MG802 3.8 30.7 1.0
O B:HOH974 4.0 26.1 1.0
O B:HOH940 4.1 31.5 1.0
CD2 B:HIS525 4.1 31.9 1.0
O B:HOH993 4.2 48.5 1.0
CG B:HIS563 4.2 28.1 1.0
ND1 B:HIS563 4.2 27.6 1.0
CG B:HIS529 4.2 30.5 1.0
ND1 B:HIS529 4.3 30.3 1.0
CB B:ASP564 4.4 27.4 1.0
NE2 B:HIS525 4.5 34.3 1.0
CB B:ASP674 4.5 29.2 1.0
O B:HOH925 4.6 29.5 1.0
CG2 B:VAL533 4.7 25.3 1.0
CA B:ASP674 4.9 28.1 1.0
O B:ASP674 4.9 30.8 1.0

Zinc binding site 3 out of 4 in 5seu

Go back to Zinc Binding Sites List in 5seu
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-6- (Trifluoromethyl)-[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 2-[2- (2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-6- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:36.9
occ:1.00
 OD2 C:ASP564 2.1 30.9 1.0
O C:HOH917 2.1 26.3 1.0
NE2 C:HIS529 2.2 30.6 1.0
NE2 C:HIS563 2.2 31.1 1.0
OD1 C:ASP674 2.3 30.9 1.0
O C:HOH941 2.4 40.7 1.0
CD2 C:HIS563 3.0 27.2 1.0
CG C:ASP674 3.1 28.7 1.0
CG C:ASP564 3.1 31.0 1.0
CD2 C:HIS529 3.1 29.1 1.0
CE1 C:HIS529 3.2 30.3 1.0
OD2 C:ASP674 3.2 33.9 1.0
CE1 C:HIS563 3.4 33.8 1.0
OD1 C:ASP564 3.5 31.4 1.0
MG C:MG802 3.8 33.1 1.0
CD2 C:HIS525 4.1 30.7 1.0
O C:HOH988 4.2 28.0 1.0
O C:HOH950 4.2 33.2 1.0
CG C:HIS563 4.2 29.1 1.0
CG C:HIS529 4.3 27.8 1.0
ND1 C:HIS529 4.3 29.1 1.0
CB C:ASP564 4.3 29.5 1.0
ND1 C:HIS563 4.4 29.0 1.0
NE2 C:HIS525 4.4 34.0 1.0
O C:HOH991 4.4 42.5 1.0
CB C:ASP674 4.5 32.4 1.0
O C:HOH942 4.6 33.8 1.0
CG2 C:VAL533 4.8 34.5 1.0
CA C:ASP674 4.9 33.6 1.0
O C:ASP674 4.9 33.1 1.0

Zinc binding site 4 out of 4 in 5seu

Go back to Zinc Binding Sites List in 5seu
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-6- (Trifluoromethyl)-[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 2-[2- (2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-6- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:53.6
occ:1.00
 O D:HOH922 2.0 43.2 1.0
O D:HOH924 2.1 37.8 1.0
NE2 D:HIS563 2.2 43.9 1.0
OD1 D:ASP674 2.2 51.1 1.0
NE2 D:HIS529 2.3 42.2 1.0
OD2 D:ASP564 2.3 57.4 1.0
CD2 D:HIS563 3.0 46.1 1.0
CD2 D:HIS529 3.1 48.5 1.0
CG D:ASP674 3.2 45.1 1.0
CG D:ASP564 3.2 47.3 1.0
CE1 D:HIS563 3.3 47.1 1.0
CE1 D:HIS529 3.3 50.1 1.0
OD2 D:ASP674 3.5 50.8 1.0
MG D:MG802 3.7 48.2 1.0
OD1 D:ASP564 3.7 48.7 1.0
O D:HOH910 4.0 48.1 1.0
O D:HOH915 4.2 37.6 1.0
CB D:ASP564 4.2 46.7 1.0
CD2 D:HIS525 4.2 48.3 1.0
CG D:HIS563 4.2 44.8 1.0
CG D:HIS529 4.3 43.0 1.0
ND1 D:HIS563 4.3 42.5 1.0
ND1 D:HIS529 4.4 43.2 1.0
CB D:ASP674 4.5 46.3 1.0
NE2 D:HIS525 4.6 53.8 1.0
O D:HOH908 4.6 38.2 1.0
CG2 D:VAL533 4.7 44.5 1.0
CA D:ASP674 4.8 48.6 1.0
O D:ASP674 4.9 53.6 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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