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Zinc in PDB 5sf0: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(3-Pyridin-2-Yl-1H-Pyrazol-5-Yl) Pyrazole-3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(3-Pyridin-2-Yl-1H-Pyrazol-5-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-(3-Pyridin-2-Yl-1H-Pyrazol-5-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-(3-Pyridin-2-Yl-1H-Pyrazol-5-Yl) Pyrazole-3-Carboxamide, PDB code: 5sf0 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) 43.50 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.588, 134.588, 234.418, 90, 90, 120
R / Rfree (%) 19.7 / 24.2

Other elements in 5sf0:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-(3-Pyridin-2-Yl-1H-Pyrazol-5-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-(3-Pyridin-2-Yl-1H-Pyrazol-5-Yl) Pyrazole-3-Carboxamide (pdb code 5sf0). 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-(3-Pyridin-2-Yl-1H-Pyrazol-5-Yl) Pyrazole-3-Carboxamide, PDB code: 5sf0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sf0

Go back to Zinc Binding Sites List in 5sf0
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-(3-Pyridin-2-Yl-1H-Pyrazol-5-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-(3-Pyridin-2-Yl-1H-Pyrazol-5-Yl) Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:32.0
occ:1.00
 NE2 A:HIS529 2.1 28.1 1.0
OD1 A:ASP674 2.1 33.7 1.0
OD2 A:ASP564 2.1 26.4 1.0
NE2 A:HIS563 2.2 27.3 1.0
O A:HOH953 2.3 24.0 1.0
O A:HOH998 2.3 30.1 1.0
CG A:ASP674 3.0 29.7 1.0
CD2 A:HIS529 3.1 27.0 1.0
CD2 A:HIS563 3.1 28.1 1.0
CE1 A:HIS529 3.1 27.5 1.0
CG A:ASP564 3.2 24.1 1.0
CE1 A:HIS563 3.2 29.4 1.0
OD2 A:ASP674 3.2 33.8 1.0
OD1 A:ASP564 3.7 24.5 1.0
MG A:MG802 3.9 23.9 1.0
O A:HOH993 4.2 20.9 1.0
ND1 A:HIS529 4.2 28.3 1.0
CG A:HIS529 4.2 27.2 1.0
CG A:HIS563 4.2 28.1 1.0
ND1 A:HIS563 4.2 27.9 1.0
CD2 A:HIS525 4.3 29.4 1.0
CB A:ASP564 4.3 23.6 1.0
CB A:ASP674 4.4 27.9 1.0
O A:HOH976 4.4 36.9 1.0
NE2 A:HIS525 4.5 30.0 1.0
O A:HOH926 4.6 23.5 1.0
CG2 A:VAL533 4.6 23.8 1.0
CA A:ASP674 4.8 26.8 1.0
O A:ASP674 4.8 26.3 1.0

Zinc binding site 2 out of 4 in 5sf0

Go back to Zinc Binding Sites List in 5sf0
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-(3-Pyridin-2-Yl-1H-Pyrazol-5-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-(3-Pyridin-2-Yl-1H-Pyrazol-5-Yl) Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:29.7
occ:1.00
 O B:HOH916 2.1 16.9 1.0
OD1 B:ASP674 2.1 22.2 1.0
NE2 B:HIS529 2.1 22.2 1.0
NE2 B:HIS563 2.2 22.8 1.0
OD2 B:ASP564 2.2 25.1 1.0
O B:HOH973 2.3 28.2 1.0
CG B:ASP674 3.0 24.2 1.0
CD2 B:HIS563 3.1 23.8 1.0
CD2 B:HIS529 3.1 22.5 1.0
CG B:ASP564 3.1 24.1 1.0
CE1 B:HIS529 3.2 24.8 1.0
OD2 B:ASP674 3.2 25.1 1.0
CE1 B:HIS563 3.2 23.3 1.0
OD1 B:ASP564 3.6 24.3 1.0
MG B:MG802 3.8 21.0 1.0
O B:HOH959 3.9 20.0 1.0
CD2 B:HIS525 4.2 28.6 1.0
O B:HOH947 4.2 33.0 1.0
CG B:HIS563 4.2 23.5 1.0
ND1 B:HIS529 4.3 22.5 1.0
CG B:HIS529 4.3 21.9 1.0
ND1 B:HIS563 4.3 23.0 1.0
CB B:ASP564 4.3 25.6 1.0
CB B:ASP674 4.4 24.5 1.0
NE2 B:HIS525 4.5 29.5 1.0
O B:HOH1018 4.5 58.8 1.0
CG2 B:VAL533 4.7 23.6 1.0
O B:HOH948 4.8 23.1 1.0
CA B:ASP674 4.8 25.5 1.0
O B:ASP674 4.9 26.6 1.0

Zinc binding site 3 out of 4 in 5sf0

Go back to Zinc Binding Sites List in 5sf0
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-(3-Pyridin-2-Yl-1H-Pyrazol-5-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-(3-Pyridin-2-Yl-1H-Pyrazol-5-Yl) Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:30.7
occ:1.00
 OD2 C:ASP564 2.1 23.9 1.0
OD1 C:ASP674 2.1 25.0 1.0
NE2 C:HIS529 2.1 25.7 1.0
O C:HOH943 2.2 20.2 1.0
O C:HOH961 2.3 38.2 1.0
NE2 C:HIS563 2.3 26.8 1.0
CG C:ASP674 3.0 26.6 1.0
CD2 C:HIS563 3.1 25.2 1.0
CG C:ASP564 3.1 22.6 1.0
CE1 C:HIS529 3.1 25.6 1.0
CD2 C:HIS529 3.1 25.4 1.0
OD2 C:ASP674 3.3 28.4 1.0
CE1 C:HIS563 3.4 29.4 1.0
OD1 C:ASP564 3.7 22.0 1.0
MG C:MG802 3.7 23.8 1.0
CD2 C:HIS525 4.1 32.9 1.0
O C:HOH991 4.1 34.7 1.0
O C:HOH980 4.1 24.1 1.0
ND1 C:HIS529 4.2 24.8 1.0
CG C:HIS529 4.3 24.7 1.0
CB C:ASP564 4.3 22.9 1.0
CG C:HIS563 4.3 25.8 1.0
CB C:ASP674 4.4 28.9 1.0
NE2 C:HIS525 4.4 35.7 1.0
ND1 C:HIS563 4.4 26.7 1.0
O C:HOH927 4.6 27.6 1.0
O C:ASP674 4.8 29.9 1.0
CA C:ASP674 4.8 30.5 1.0
CG2 C:VAL533 4.8 23.9 1.0
O C:HOH1020 5.0 43.8 1.0
O C:HOH973 5.0 18.7 1.0

Zinc binding site 4 out of 4 in 5sf0

Go back to Zinc Binding Sites List in 5sf0
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-(3-Pyridin-2-Yl-1H-Pyrazol-5-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-(3-Pyridin-2-Yl-1H-Pyrazol-5-Yl) Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:37.9
occ:1.00
 O D:HOH933 2.0 34.3 1.0
OD2 D:ASP564 2.1 43.2 1.0
NE2 D:HIS529 2.2 31.6 1.0
O D:HOH962 2.2 37.1 1.0
NE2 D:HIS563 2.2 26.8 1.0
OD1 D:ASP674 2.2 35.2 1.0
CD2 D:HIS563 3.0 32.6 1.0
CD2 D:HIS529 3.1 32.5 1.0
CG D:ASP564 3.1 34.4 1.0
CG D:ASP674 3.2 32.6 1.0
CE1 D:HIS529 3.2 31.6 1.0
CE1 D:HIS563 3.3 33.1 1.0
OD2 D:ASP674 3.4 33.7 1.0
OD1 D:ASP564 3.7 36.2 1.0
MG D:MG802 3.8 43.8 1.0
O D:HOH954 4.1 32.8 1.0
O D:HOH945 4.2 41.4 1.0
CD2 D:HIS525 4.2 37.7 1.0
CG D:HIS563 4.2 31.3 1.0
CG D:HIS529 4.3 31.2 1.0
CB D:ASP564 4.3 34.3 1.0
ND1 D:HIS529 4.3 30.9 1.0
ND1 D:HIS563 4.4 31.4 1.0
CB D:ASP674 4.5 34.4 1.0
O D:HOH906 4.6 38.5 1.0
NE2 D:HIS525 4.6 40.9 1.0
CG2 D:VAL533 4.7 33.9 1.0
O D:ASP674 4.7 34.6 1.0
CA D:ASP674 4.8 35.1 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 04:50:43 2024

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