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Zinc in PDB 5siy: Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine, PDB code: 5siy was solved by C.Joseph, J.Benz, A.Flohr, L.Gobbi, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.41 / 2.03
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.911, 134.911, 236.562, 90, 90, 120
R / Rfree (%) 17.5 / 22.1

Other elements in 5siy:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine (pdb code 5siy). 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- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine, PDB code: 5siy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5siy

Go back to Zinc Binding Sites List in 5siy
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine


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- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:31.5
occ:1.00
 O A:HOH937 2.1 25.0 1.0
NE2 A:HIS529 2.1 30.8 1.0
OD2 A:ASP564 2.1 26.5 1.0
NE2 A:HIS563 2.2 26.9 1.0
O A:HOH969 2.2 40.2 1.0
OD1 A:ASP674 2.3 28.6 1.0
CD2 A:HIS563 3.0 26.2 1.0
CD2 A:HIS529 3.0 27.9 1.0
CG A:ASP564 3.0 26.6 1.0
CG A:ASP674 3.1 29.6 1.0
CE1 A:HIS529 3.1 31.5 1.0
OD2 A:ASP674 3.3 30.5 1.0
CE1 A:HIS563 3.3 33.7 1.0
OD1 A:ASP564 3.5 24.4 1.0
MG A:MG802 3.8 28.4 1.0
CD2 A:HIS525 4.1 28.3 1.0
CG A:HIS563 4.2 29.3 1.0
O A:HOH982 4.2 27.1 1.0
CG A:HIS529 4.2 29.1 1.0
ND1 A:HIS529 4.2 25.1 1.0
CB A:ASP564 4.3 28.1 1.0
ND1 A:HIS563 4.3 28.0 1.0
O A:HOH940 4.4 36.4 1.0
NE2 A:HIS525 4.5 30.5 1.0
CB A:ASP674 4.5 26.0 1.0
O A:HOH918 4.5 24.2 1.0
CG2 A:VAL533 4.8 26.0 1.0
O A:ASP674 4.9 24.4 1.0
CA A:ASP674 4.9 26.1 1.0

Zinc binding site 2 out of 4 in 5siy

Go back to Zinc Binding Sites List in 5siy
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine


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- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:30.4
occ:1.00
 O B:HOH944 2.0 23.9 1.0
NE2 B:HIS563 2.1 23.9 1.0
OD1 B:ASP674 2.2 24.3 1.0
OD2 B:ASP564 2.2 24.8 1.0
NE2 B:HIS529 2.2 24.6 1.0
O B:HOH978 2.6 32.6 1.0
CD2 B:HIS563 3.1 25.5 1.0
CG B:ASP674 3.1 26.2 1.0
CD2 B:HIS529 3.1 26.3 1.0
CE1 B:HIS563 3.1 25.2 1.0
CG B:ASP564 3.2 26.5 1.0
CE1 B:HIS529 3.2 26.6 1.0
OD2 B:ASP674 3.3 27.4 1.0
OD1 B:ASP564 3.7 28.2 1.0
MG B:MG802 3.7 25.6 1.0
CD2 B:HIS525 4.1 26.4 1.0
O B:HOH998 4.1 23.9 1.0
O B:HOH933 4.1 37.5 1.0
CG B:HIS563 4.2 25.6 1.0
ND1 B:HIS563 4.2 24.2 1.0
CG B:HIS529 4.3 25.3 1.0
CB B:ASP564 4.3 24.2 1.0
ND1 B:HIS529 4.3 25.3 1.0
NE2 B:HIS525 4.4 33.4 1.0
CB B:ASP674 4.4 25.1 1.0
O B:HOH930 4.6 24.6 1.0
CG2 B:VAL533 4.6 23.1 1.0
CA B:ASP674 4.9 23.9 1.0
O B:ASP674 4.9 25.6 1.0

Zinc binding site 3 out of 4 in 5siy

Go back to Zinc Binding Sites List in 5siy
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine


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- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:31.8
occ:1.00
 O C:HOH948 2.0 21.8 1.0
NE2 C:HIS529 2.2 31.2 1.0
OD1 C:ASP674 2.2 27.3 1.0
OD2 C:ASP564 2.2 27.6 1.0
O C:HOH995 2.3 35.8 1.0
NE2 C:HIS563 2.3 24.4 1.0
CD2 C:HIS563 3.1 25.3 1.0
CG C:ASP564 3.1 26.0 1.0
CG C:ASP674 3.2 26.9 1.0
CE1 C:HIS529 3.2 29.6 1.0
CD2 C:HIS529 3.2 29.0 1.0
CE1 C:HIS563 3.4 28.7 1.0
OD2 C:ASP674 3.4 30.2 1.0
OD1 C:ASP564 3.6 26.1 1.0
MG C:MG802 3.7 27.4 1.0
CD2 C:HIS525 4.1 29.5 1.0
O C:HOH1005 4.2 29.6 1.0
ND1 C:HIS529 4.3 26.8 1.0
CG C:HIS563 4.3 25.1 1.0
CG C:HIS529 4.3 28.0 1.0
CB C:ASP564 4.3 26.1 1.0
O C:HOH952 4.3 40.0 1.0
ND1 C:HIS563 4.4 26.2 1.0
CB C:ASP674 4.5 26.1 1.0
NE2 C:HIS525 4.5 31.9 1.0
O C:HOH937 4.6 26.9 1.0
CG2 C:VAL533 4.7 25.5 1.0
CA C:ASP674 4.8 29.8 1.0
O C:ASP674 4.9 26.9 1.0

Zinc binding site 4 out of 4 in 5siy

Go back to Zinc Binding Sites List in 5siy
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine


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- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:39.2
occ:1.00
 O D:HOH927 2.0 30.1 1.0
NE2 D:HIS529 2.1 34.1 1.0
NE2 D:HIS563 2.1 34.3 1.0
OD2 D:ASP564 2.2 38.6 1.0
OD1 D:ASP674 2.2 33.5 1.0
O D:HOH935 2.2 37.4 1.0
CD2 D:HIS563 3.0 33.2 1.0
CE1 D:HIS529 3.1 30.3 1.0
CD2 D:HIS529 3.1 35.2 1.0
CG D:ASP674 3.1 33.2 1.0
CG D:ASP564 3.2 33.7 1.0
CE1 D:HIS563 3.2 33.8 1.0
OD2 D:ASP674 3.3 36.5 1.0
OD1 D:ASP564 3.7 33.3 1.0
MG D:MG802 3.7 34.1 1.0
O D:HOH962 4.0 34.9 1.0
CD2 D:HIS525 4.1 35.9 1.0
O D:HOH921 4.2 43.0 1.0
CG D:HIS563 4.2 30.4 1.0
ND1 D:HIS529 4.2 31.7 1.0
CG D:HIS529 4.3 32.8 1.0
ND1 D:HIS563 4.3 33.9 1.0
NE2 D:HIS525 4.3 42.5 1.0
CB D:ASP564 4.3 34.0 1.0
CB D:ASP674 4.5 31.4 1.0
O D:HOH912 4.7 30.1 1.0
CG2 D:VAL533 4.8 38.5 1.0
O D:ASP674 4.8 36.5 1.0
CA D:ASP674 4.9 33.5 1.0

Reference:

A.Flohr, D.Schlatter, B.Kuhn, M.G.Rudolph. Crystal Structure of A Human Phosphodiesterase 10 Complex To Be Published.
Page generated: Mon Oct 28 05:52:52 2024

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