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Zinc in PDB 5sju: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide, PDB code: 5sju was solved by C.Joseph, J.Benz, A.Flohr, M.Koerner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.63 / 1.97
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.633, 135.633, 235.654, 90, 90, 120
R / Rfree (%) 17.6 / 22

Other elements in 5sju:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide 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 6- Cyclopropyl-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide (pdb code 5sju). 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- Cyclopropyl-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide, PDB code: 5sju:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sju

Go back to Zinc Binding Sites List in 5sju
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide


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- Cyclopropyl-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:31.8
occ:1.00
 O A:HOH997 2.1 26.0 1.0
OD2 A:ASP564 2.1 26.0 1.0
NE2 A:HIS529 2.2 27.8 1.0
NE2 A:HIS563 2.2 25.1 1.0
OD1 A:ASP674 2.2 29.3 1.0
O A:HOH976 2.5 38.2 1.0
CD2 A:HIS563 3.1 24.2 1.0
CD2 A:HIS529 3.1 30.7 1.0
CG A:ASP564 3.1 26.9 1.0
CG A:ASP674 3.1 28.7 1.0
CE1 A:HIS529 3.2 26.7 1.0
CE1 A:HIS563 3.3 29.4 1.0
OD2 A:ASP674 3.4 33.5 1.0
OD1 A:ASP564 3.6 25.6 1.0
MG A:MG802 3.7 25.8 1.0
CD2 A:HIS525 4.1 30.9 1.0
O A:HOH971 4.1 32.0 1.0
O A:HOH1028 4.2 26.5 1.0
CG A:HIS563 4.2 26.7 1.0
CG A:HIS529 4.3 28.5 1.0
ND1 A:HIS529 4.3 25.1 1.0
CB A:ASP564 4.3 26.8 1.0
ND1 A:HIS563 4.3 26.9 1.0
NE2 A:HIS525 4.5 29.4 1.0
CB A:ASP674 4.5 27.6 1.0
O A:HOH1018 4.5 45.9 1.0
O A:HOH934 4.5 23.6 1.0
O A:ASP674 4.8 26.9 1.0
CG2 A:VAL533 4.8 25.3 1.0
CA A:ASP674 4.9 25.1 1.0

Zinc binding site 2 out of 4 in 5sju

Go back to Zinc Binding Sites List in 5sju
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide


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- Cyclopropyl-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:30.4
occ:1.00
 O B:HOH985 2.0 21.8 1.0
OD2 B:ASP564 2.2 23.7 1.0
OD1 B:ASP674 2.2 26.0 1.0
NE2 B:HIS529 2.2 21.8 1.0
NE2 B:HIS563 2.2 21.3 1.0
O B:HOH989 2.4 44.0 1.0
CD2 B:HIS563 3.1 22.1 1.0
CG B:ASP674 3.1 28.1 1.0
CD2 B:HIS529 3.1 25.3 1.0
CG B:ASP564 3.1 22.9 1.0
CE1 B:HIS529 3.2 25.2 1.0
CE1 B:HIS563 3.3 24.6 1.0
OD2 B:ASP674 3.4 27.9 1.0
OD1 B:ASP564 3.6 24.3 1.0
MG B:MG802 3.7 24.2 1.0
O B:HOH1020 4.0 24.6 1.0
O B:HOH980 4.0 28.8 1.0
CD2 B:HIS525 4.1 30.0 1.0
CG B:HIS563 4.2 23.9 1.0
CG B:HIS529 4.3 23.4 1.0
CB B:ASP564 4.3 21.4 1.0
ND1 B:HIS563 4.3 24.2 1.0
ND1 B:HIS529 4.4 23.2 1.0
CB B:ASP674 4.4 24.2 1.0
O B:HOH991 4.5 39.9 1.0
NE2 B:HIS525 4.5 29.1 1.0
O B:HOH960 4.6 23.9 1.0
CG2 B:VAL533 4.8 25.0 1.0
O B:ASP674 4.8 27.0 1.0
CA B:ASP674 4.8 25.4 1.0

Zinc binding site 3 out of 4 in 5sju

Go back to Zinc Binding Sites List in 5sju
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide


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- Cyclopropyl-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:31.9
occ:1.00
 O C:HOH967 2.1 22.8 1.0
NE2 C:HIS529 2.2 26.0 1.0
NE2 C:HIS563 2.2 28.6 1.0
OD1 C:ASP674 2.2 24.6 1.0
OD2 C:ASP564 2.2 25.8 1.0
O C:HOH932 2.6 48.4 1.0
CD2 C:HIS563 3.1 26.3 1.0
CG C:ASP674 3.1 28.1 1.0
CD2 C:HIS529 3.1 27.2 1.0
CG C:ASP564 3.2 28.6 1.0
CE1 C:HIS529 3.2 29.7 1.0
CE1 C:HIS563 3.2 24.6 1.0
OD2 C:ASP674 3.3 34.5 1.0
OD1 C:ASP564 3.7 25.9 1.0
MG C:MG802 3.7 25.5 1.0
CD2 C:HIS525 4.1 29.4 1.0
O C:HOH1047 4.2 25.1 1.0
CG C:HIS563 4.2 26.5 1.0
O C:HOH1021 4.3 33.5 1.0
CG C:HIS529 4.3 28.6 1.0
ND1 C:HIS563 4.3 24.1 1.0
ND1 C:HIS529 4.3 27.3 1.0
CB C:ASP564 4.4 25.2 1.0
CB C:ASP674 4.4 26.0 1.0
NE2 C:HIS525 4.5 33.0 1.0
O C:HOH964 4.5 29.0 1.0
O C:HOH1037 4.6 43.3 1.0
CA C:ASP674 4.8 26.3 1.0
CG2 C:VAL533 4.8 27.3 1.0
O C:ASP674 4.8 28.3 1.0

Zinc binding site 4 out of 4 in 5sju

Go back to Zinc Binding Sites List in 5sju
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide


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- Cyclopropyl-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:35.2
occ:1.00
 O D:HOH952 2.0 28.1 1.0
NE2 D:HIS563 2.1 25.3 1.0
NE2 D:HIS529 2.2 30.8 1.0
OD1 D:ASP674 2.2 26.6 1.0
OD2 D:ASP564 2.3 34.0 1.0
O D:HOH939 2.4 44.4 1.0
CD2 D:HIS563 3.0 28.9 1.0
CG D:ASP564 3.1 28.3 1.0
CG D:ASP674 3.1 29.7 1.0
CD2 D:HIS529 3.2 33.7 1.0
CE1 D:HIS529 3.2 30.1 1.0
CE1 D:HIS563 3.2 28.5 1.0
OD2 D:ASP674 3.3 33.0 1.0
OD1 D:ASP564 3.6 31.3 1.0
MG D:MG802 3.7 34.3 1.0
CD2 D:HIS525 4.1 35.6 1.0
O D:HOH967 4.1 29.9 1.0
CG D:HIS563 4.2 25.2 1.0
O D:HOH965 4.2 36.2 1.0
ND1 D:HIS563 4.3 26.0 1.0
CB D:ASP564 4.3 28.5 1.0
ND1 D:HIS529 4.3 30.0 1.0
CG D:HIS529 4.3 30.8 1.0
CB D:ASP674 4.5 29.8 1.0
NE2 D:HIS525 4.5 43.7 1.0
O D:HOH931 4.6 32.1 1.0
O D:ASP674 4.7 31.6 1.0
CG2 D:VAL533 4.7 31.5 1.0
CA D:ASP674 4.8 28.1 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 06:06:32 2024

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