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Zinc in PDB 5sen: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(1-Quinolin-2-Ylimidazol-4-Yl) Pyrazole-3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(1-Quinolin-2-Ylimidazol-4-Yl) Pyrazole-3-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(1-Quinolin-2-Ylimidazol-4-Yl) Pyrazole-3-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(1-Quinolin-2-Ylimidazol-4-Yl) Pyrazole-3-Carboxamide, PDB code: 5sen was solved by C.Joseph, J.U.Peters, 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) 28.45 / 2.04
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.313, 135.313, 234.965, 90, 90, 120
R / Rfree (%) 21.2 / 25.1

Other elements in 5sen:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(1-Quinolin-2-Ylimidazol-4-Yl) Pyrazole-3-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 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(1-Quinolin-2-Ylimidazol-4-Yl) Pyrazole-3-Carboxamide (pdb code 5sen). 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 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(1-Quinolin-2-Ylimidazol-4-Yl) Pyrazole-3-Carboxamide, PDB code: 5sen:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sen

Go back to Zinc Binding Sites List in 5sen
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(1-Quinolin-2-Ylimidazol-4-Yl) Pyrazole-3-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 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(1-Quinolin-2-Ylimidazol-4-Yl) Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:33.4
occ:1.00
 OD2 A:ASP564 2.1 30.8 1.0
NE2 A:HIS529 2.1 27.6 1.0
NE2 A:HIS563 2.2 28.0 1.0
OD1 A:ASP674 2.2 32.7 1.0
O A:HOH948 2.3 29.9 1.0
O A:HOH978 2.5 40.1 1.0
CD2 A:HIS563 2.9 27.5 1.0
CG A:ASP564 3.0 27.2 1.0
CD2 A:HIS529 3.1 27.8 1.0
CG A:ASP674 3.1 32.2 1.0
CE1 A:HIS529 3.1 27.6 1.0
CE1 A:HIS563 3.3 29.5 1.0
OD2 A:ASP674 3.3 39.4 1.0
OD1 A:ASP564 3.5 25.7 1.0
MG A:MG802 3.8 26.5 1.0
CG A:HIS563 4.1 27.9 1.0
CD2 A:HIS525 4.2 36.0 1.0
ND1 A:HIS529 4.2 26.4 1.0
CG A:HIS529 4.2 27.6 1.0
O A:HOH994 4.2 27.4 1.0
CB A:ASP564 4.3 27.1 1.0
ND1 A:HIS563 4.3 27.5 1.0
O A:HOH973 4.4 36.7 1.0
CB A:ASP674 4.5 31.9 1.0
NE2 A:HIS525 4.5 36.1 1.0
O A:HOH937 4.6 25.6 1.0
O A:HOH1011 4.7 46.4 1.0
CG2 A:VAL533 4.8 25.1 1.0
O A:ASP674 4.9 30.1 1.0
CA A:ASP674 4.9 29.2 1.0

Zinc binding site 2 out of 4 in 5sen

Go back to Zinc Binding Sites List in 5sen
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(1-Quinolin-2-Ylimidazol-4-Yl) Pyrazole-3-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 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(1-Quinolin-2-Ylimidazol-4-Yl) Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:32.3
occ:1.00
 OD2 B:ASP564 2.1 30.1 1.0
O B:HOH945 2.1 21.6 1.0
NE2 B:HIS563 2.1 22.0 1.0
OD1 B:ASP674 2.2 29.1 1.0
NE2 B:HIS529 2.2 23.7 1.0
O B:HOH963 2.4 34.5 1.0
CG B:ASP674 3.0 29.7 1.0
CG B:ASP564 3.1 25.7 1.0
CD2 B:HIS563 3.1 24.8 1.0
CE1 B:HIS563 3.1 24.8 1.0
CD2 B:HIS529 3.1 26.1 1.0
CE1 B:HIS529 3.2 25.9 1.0
OD2 B:ASP674 3.3 28.2 1.0
OD1 B:ASP564 3.5 25.4 1.0
MG B:MG802 3.8 27.5 1.0
O B:HOH975 4.0 22.8 1.0
CD2 B:HIS525 4.2 30.2 1.0
ND1 B:HIS563 4.2 25.5 1.0
CG B:HIS563 4.2 24.7 1.0
CG B:HIS529 4.3 26.9 1.0
ND1 B:HIS529 4.3 23.7 1.0
CB B:ASP564 4.3 26.6 1.0
NE2 B:HIS525 4.4 29.3 1.0
CB B:ASP674 4.4 28.9 1.0
O B:HOH935 4.4 30.8 1.0
O B:HOH961 4.6 28.8 1.0
CG2 B:VAL533 4.8 22.9 1.0
O B:HOH1029 4.8 54.6 1.0
CA B:ASP674 4.8 28.6 1.0
O B:ASP674 4.9 30.5 1.0

Zinc binding site 3 out of 4 in 5sen

Go back to Zinc Binding Sites List in 5sen
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(1-Quinolin-2-Ylimidazol-4-Yl) Pyrazole-3-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 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(1-Quinolin-2-Ylimidazol-4-Yl) Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:33.7
occ:1.00
 O C:HOH936 2.1 24.2 1.0
NE2 C:HIS529 2.2 27.3 1.0
OD2 C:ASP564 2.2 27.8 1.0
OD1 C:ASP674 2.2 28.6 1.0
NE2 C:HIS563 2.2 25.8 1.0
O C:HOH1000 2.2 36.3 1.0
CD2 C:HIS563 3.0 25.3 1.0
CD2 C:HIS529 3.0 26.6 1.0
CG C:ASP674 3.1 29.6 1.0
CG C:ASP564 3.1 27.0 1.0
OD2 C:ASP674 3.3 33.4 1.0
CE1 C:HIS529 3.3 27.7 1.0
CE1 C:HIS563 3.3 28.7 1.0
OD1 C:ASP564 3.6 26.1 1.0
MG C:MG802 3.9 23.4 1.0
CD2 C:HIS525 4.2 35.2 1.0
O C:HOH1008 4.2 30.1 1.0
CG C:HIS529 4.2 26.9 1.0
CG C:HIS563 4.2 27.5 1.0
ND1 C:HIS529 4.3 26.1 1.0
CB C:ASP564 4.3 25.9 1.0
ND1 C:HIS563 4.4 26.8 1.0
CB C:ASP674 4.5 31.9 1.0
O C:HOH956 4.5 39.1 1.0
NE2 C:HIS525 4.5 35.1 1.0
O C:HOH948 4.5 28.3 1.0
CG2 C:VAL533 4.7 27.6 1.0
O C:HOH1027 4.8 45.2 1.0
CA C:ASP674 4.8 31.5 1.0
O C:ASP674 5.0 34.2 1.0

Zinc binding site 4 out of 4 in 5sen

Go back to Zinc Binding Sites List in 5sen
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(1-Quinolin-2-Ylimidazol-4-Yl) Pyrazole-3-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 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(1-Quinolin-2-Ylimidazol-4-Yl) Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:36.1
occ:1.00
 OD2 D:ASP564 2.1 38.0 1.0
O D:HOH930 2.1 23.9 1.0
NE2 D:HIS529 2.2 34.0 1.0
NE2 D:HIS563 2.2 30.8 1.0
OD1 D:ASP674 2.3 34.1 1.0
O D:HOH972 2.4 37.3 1.0
CD2 D:HIS563 2.9 32.6 1.0
CD2 D:HIS529 3.1 34.5 1.0
CG D:ASP564 3.1 34.2 1.0
CG D:ASP674 3.2 35.6 1.0
CE1 D:HIS529 3.2 35.4 1.0
OD2 D:ASP674 3.4 41.2 1.0
CE1 D:HIS563 3.4 34.3 1.0
OD1 D:ASP564 3.6 32.0 1.0
MG D:MG802 3.9 34.6 1.0
CB D:ASP564 4.2 34.2 1.0
CG D:HIS563 4.2 31.0 1.0
CD2 D:HIS525 4.2 42.4 1.0
CG D:HIS529 4.2 33.8 1.0
ND1 D:HIS529 4.3 33.8 1.0
O D:HOH962 4.4 29.9 1.0
ND1 D:HIS563 4.4 30.5 1.0
O D:HOH954 4.5 35.5 1.0
CB D:ASP674 4.5 36.8 1.0
NE2 D:HIS525 4.6 39.9 1.0
O D:HOH928 4.7 34.7 1.0
CG2 D:VAL533 4.7 35.3 1.0
O D:ASP674 4.8 38.5 1.0
CA D:ASP674 4.9 35.3 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 04:43:23 2024

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