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Zinc in PDB 5se5: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-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-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-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-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide, PDB code: 5se5 was solved by C.Joseph, K.Groebke-Zbinden, 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) 43.40 / 2.08
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.91, 134.91, 234.914, 90, 90, 120
R / Rfree (%) 18.6 / 22.6

Other elements in 5se5:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-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-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide (pdb code 5se5). 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-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide, PDB code: 5se5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5se5

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-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-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:33.1
occ:1.00
 NE2 A:HIS563 2.1 28.0 1.0
NE2 A:HIS529 2.1 29.5 1.0
OD2 A:ASP564 2.1 32.1 1.0
OD1 A:ASP674 2.2 30.5 1.0
O A:HOH951 2.2 30.4 1.0
O A:HOH995 2.4 42.2 1.0
CD2 A:HIS563 3.0 27.6 1.0
CG A:ASP564 3.0 29.4 1.0
CD2 A:HIS529 3.1 28.9 1.0
CG A:ASP674 3.1 30.3 1.0
CE1 A:HIS529 3.1 28.3 1.0
CE1 A:HIS563 3.1 29.2 1.0
OD2 A:ASP674 3.3 35.0 1.0
OD1 A:ASP564 3.5 27.4 1.0
MG A:MG802 3.8 28.8 1.0
O A:HOH1007 4.1 29.5 1.0
CG A:HIS563 4.1 27.9 1.0
CD2 A:HIS525 4.2 31.7 1.0
ND1 A:HIS563 4.2 27.2 1.0
ND1 A:HIS529 4.2 28.0 1.0
CG A:HIS529 4.2 28.9 1.0
O A:HOH964 4.2 31.5 1.0
CB A:ASP564 4.2 26.6 1.0
CB A:ASP674 4.4 28.7 1.0
NE2 A:HIS525 4.5 30.7 1.0
O A:HOH922 4.5 25.4 1.0
CG2 A:VAL533 4.7 24.3 1.0
O A:ASP674 4.8 28.8 1.0
CA A:ASP674 4.8 28.3 1.0
O A:HOH1012 4.9 58.0 1.0

Zinc binding site 2 out of 4 in 5se5

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-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-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:32.8
occ:1.00
 NE2 B:HIS563 2.0 24.2 1.0
O B:HOH946 2.1 23.1 1.0
NE2 B:HIS529 2.2 28.3 1.0
OD2 B:ASP564 2.2 28.3 1.0
OD1 B:ASP674 2.2 29.4 1.0
O B:HOH961 2.6 43.9 1.0
CD2 B:HIS563 3.0 25.8 1.0
CG B:ASP674 3.0 30.6 1.0
CE1 B:HIS563 3.1 26.3 1.0
CG B:ASP564 3.1 27.3 1.0
CD2 B:HIS529 3.1 29.5 1.0
CE1 B:HIS529 3.2 31.4 1.0
OD2 B:ASP674 3.3 30.8 1.0
OD1 B:ASP564 3.5 27.6 1.0
MG B:MG802 3.8 26.4 1.0
O B:HOH1002 4.0 26.2 1.0
CD2 B:HIS525 4.1 29.5 1.0
CG B:HIS563 4.1 25.9 1.0
O B:HOH967 4.1 33.1 1.0
ND1 B:HIS563 4.2 25.7 1.0
ND1 B:HIS529 4.3 29.5 1.0
CG B:HIS529 4.3 29.5 1.0
CB B:ASP564 4.3 28.0 1.0
CB B:ASP674 4.4 28.9 1.0
NE2 B:HIS525 4.5 29.0 1.0
O B:HOH936 4.5 25.3 1.0
CG2 B:VAL533 4.7 28.6 1.0
O B:HOH1014 4.8 53.5 1.0
CA B:ASP674 4.8 29.2 1.0
O B:ASP674 4.8 28.9 1.0

Zinc binding site 3 out of 4 in 5se5

Go back to Zinc Binding Sites List in 5se5
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-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-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:37.7
occ:1.00
 O C:HOH959 2.0 30.4 1.0
NE2 C:HIS563 2.1 27.5 1.0
OD2 C:ASP564 2.2 32.4 1.0
NE2 C:HIS529 2.2 30.2 1.0
OD1 C:ASP674 2.2 31.0 1.0
O C:HOH973 2.7 48.4 1.0
CD2 C:HIS563 3.0 28.1 1.0
CD2 C:HIS529 3.1 32.4 1.0
CG C:ASP674 3.1 33.4 1.0
CE1 C:HIS563 3.1 29.3 1.0
CG C:ASP564 3.2 30.5 1.0
CE1 C:HIS529 3.2 35.5 1.0
OD2 C:ASP674 3.3 35.4 1.0
OD1 C:ASP564 3.6 33.4 1.0
MG C:MG802 3.7 31.1 1.0
CD2 C:HIS525 4.1 38.8 1.0
CG C:HIS563 4.1 29.6 1.0
ND1 C:HIS563 4.2 26.7 1.0
CG C:HIS529 4.2 33.4 1.0
ND1 C:HIS529 4.3 32.5 1.0
O C:HOH994 4.3 29.7 1.0
O C:HOH990 4.3 40.0 1.0
CB C:ASP564 4.3 29.9 1.0
CB C:ASP674 4.4 35.7 1.0
O C:HOH932 4.5 29.8 1.0
NE2 C:HIS525 4.5 38.0 1.0
O C:ASP674 4.8 36.9 1.0
CG2 C:VAL533 4.8 31.9 1.0
CA C:ASP674 4.8 35.1 1.0

Zinc binding site 4 out of 4 in 5se5

Go back to Zinc Binding Sites List in 5se5
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-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-[1-Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:42.4
occ:1.00
 O D:HOH920 2.1 29.1 1.0
NE2 D:HIS563 2.1 32.0 1.0
NE2 D:HIS529 2.2 38.9 1.0
OD2 D:ASP564 2.2 41.1 1.0
OD1 D:ASP674 2.2 35.1 1.0
O D:HOH957 2.5 39.0 1.0
CD2 D:HIS563 2.9 33.5 1.0
CG D:ASP674 3.1 36.9 1.0
CG D:ASP564 3.1 35.4 1.0
CD2 D:HIS529 3.1 38.2 1.0
CE1 D:HIS529 3.2 39.3 1.0
CE1 D:HIS563 3.2 34.2 1.0
OD2 D:ASP674 3.3 40.4 1.0
OD1 D:ASP564 3.6 33.2 1.0
MG D:MG802 3.8 36.0 1.0
CD2 D:HIS525 4.1 44.5 1.0
O D:HOH932 4.1 44.8 1.0
CG D:HIS563 4.2 32.1 1.0
O D:HOH979 4.2 37.1 1.0
ND1 D:HIS563 4.3 32.9 1.0
CB D:ASP564 4.3 34.9 1.0
CG D:HIS529 4.3 37.2 1.0
ND1 D:HIS529 4.3 39.8 1.0
CB D:ASP674 4.4 34.5 1.0
O D:HOH923 4.5 33.4 1.0
NE2 D:HIS525 4.5 44.6 1.0
O D:ASP674 4.8 34.7 1.0
CG2 D:VAL533 4.8 37.1 1.0
CA D:ASP674 4.8 34.5 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 04:34:58 2024

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