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Zinc in PDB 5sfo: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(1-Methyl-4-Phenylimidazol-2- Yl)Ethyl]Pyrazole-3-Carboxamide

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

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(1-Methyl-4-Phenylimidazol-2- Yl)Ethyl]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-[2-(1-Methyl-4-Phenylimidazol-2- Yl)Ethyl]Pyrazole-3-Carboxamide, PDB code: 5sfo was solved by C.Joseph, M.Koerner, 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) 43.58 / 1.96
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.004, 135.004, 234.814, 90, 90, 120
R / Rfree (%) 17.6 / 21.8

Other elements in 5sfo:

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

Zinc binding site 1 out of 4 in 5sfo

Go back to Zinc Binding Sites List in 5sfo
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-[2-(1-Methyl-4-Phenylimidazol-2- Yl)Ethyl]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-[2-(1-Methyl-4-Phenylimidazol-2- Yl)Ethyl]Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:27.9
occ:1.00
 OD2 A:ASP564 2.1 24.2 1.0
O A:HOH976 2.1 24.2 1.0
NE2 A:HIS529 2.1 24.6 1.0
NE2 A:HIS563 2.2 23.3 1.0
OD1 A:ASP674 2.2 24.5 1.0
O A:HOH1018 2.4 32.7 1.0
CD2 A:HIS563 3.0 21.7 1.0
CD2 A:HIS529 3.1 21.9 1.0
CG A:ASP564 3.1 25.7 1.0
CG A:ASP674 3.1 25.6 1.0
CE1 A:HIS529 3.1 24.6 1.0
CE1 A:HIS563 3.3 25.9 1.0
OD2 A:ASP674 3.4 26.6 1.0
OD1 A:ASP564 3.6 22.4 1.0
MG A:MG802 3.7 23.9 1.0
CD2 A:HIS525 4.1 25.9 1.0
O A:HOH995 4.1 23.3 1.0
CG A:HIS563 4.2 21.6 1.0
CG A:HIS529 4.2 22.2 1.0
ND1 A:HIS529 4.3 20.8 1.0
O A:HOH950 4.3 26.8 1.0
ND1 A:HIS563 4.3 24.4 1.0
CB A:ASP564 4.3 22.8 1.0
NE2 A:HIS525 4.4 27.1 1.0
O A:HOH933 4.4 21.9 1.0
CB A:ASP674 4.5 24.7 1.0
O A:HOH1022 4.5 51.6 1.0
CG2 A:VAL533 4.7 19.6 1.0
O A:ASP674 4.8 23.6 1.0
CA A:ASP674 4.8 22.8 1.0

Zinc binding site 2 out of 4 in 5sfo

Go back to Zinc Binding Sites List in 5sfo
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-[2-(1-Methyl-4-Phenylimidazol-2- Yl)Ethyl]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-[2-(1-Methyl-4-Phenylimidazol-2- Yl)Ethyl]Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:26.7
occ:1.00
 O B:HOH939 2.0 19.5 1.0
OD1 B:ASP674 2.1 19.2 1.0
NE2 B:HIS563 2.1 20.9 1.0
OD2 B:ASP564 2.2 20.5 1.0
NE2 B:HIS529 2.2 20.2 1.0
O B:HOH979 2.4 33.8 1.0
CG B:ASP674 3.0 22.6 1.0
CD2 B:HIS563 3.0 20.5 1.0
CD2 B:HIS529 3.1 20.2 1.0
CG B:ASP564 3.1 20.4 1.0
CE1 B:HIS563 3.2 20.9 1.0
CE1 B:HIS529 3.2 21.3 1.0
OD2 B:ASP674 3.3 21.9 1.0
OD1 B:ASP564 3.6 21.6 1.0
MG B:MG802 3.7 20.9 1.0
CD2 B:HIS525 4.0 22.8 1.0
O B:HOH999 4.0 17.5 1.0
CG B:HIS563 4.2 20.9 1.0
O B:HOH962 4.2 27.5 1.0
ND1 B:HIS563 4.3 19.8 1.0
CG B:HIS529 4.3 21.4 1.0
CB B:ASP564 4.3 18.8 1.0
ND1 B:HIS529 4.3 19.5 1.0
NE2 B:HIS525 4.4 25.1 1.0
CB B:ASP674 4.4 24.8 1.0
O B:HOH955 4.5 21.9 1.0
O B:HOH1051 4.6 47.5 1.0
CG2 B:VAL533 4.7 20.2 1.0
CA B:ASP674 4.8 21.9 1.0
O B:ASP674 4.8 22.6 1.0

Zinc binding site 3 out of 4 in 5sfo

Go back to Zinc Binding Sites List in 5sfo
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-[2-(1-Methyl-4-Phenylimidazol-2- Yl)Ethyl]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-[2-(1-Methyl-4-Phenylimidazol-2- Yl)Ethyl]Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:27.6
occ:1.00
 O C:HOH998 2.0 22.7 1.0
NE2 C:HIS529 2.2 21.8 1.0
NE2 C:HIS563 2.2 21.2 1.0
OD2 C:ASP564 2.2 20.7 1.0
OD1 C:ASP674 2.2 20.8 1.0
O C:HOH1014 2.5 33.2 1.0
CD2 C:HIS563 3.0 22.1 1.0
CD2 C:HIS529 3.0 22.2 1.0
CG C:ASP674 3.1 23.8 1.0
CG C:ASP564 3.1 21.0 1.0
CE1 C:HIS529 3.3 23.6 1.0
CE1 C:HIS563 3.3 22.9 1.0
OD2 C:ASP674 3.3 26.9 1.0
OD1 C:ASP564 3.6 21.0 1.0
MG C:MG802 3.8 22.9 1.0
CD2 C:HIS525 4.1 28.3 1.0
O C:HOH1033 4.1 20.9 1.0
CG C:HIS563 4.2 21.4 1.0
CG C:HIS529 4.2 21.8 1.0
ND1 C:HIS563 4.3 22.2 1.0
ND1 C:HIS529 4.3 21.6 1.0
CB C:ASP564 4.3 20.7 1.0
NE2 C:HIS525 4.4 25.8 1.0
O C:HOH1018 4.4 31.9 1.0
CB C:ASP674 4.4 24.9 1.0
O C:HOH961 4.6 24.7 1.0
O C:HOH1052 4.7 47.7 1.0
CG2 C:VAL533 4.7 22.2 1.0
CA C:ASP674 4.8 25.8 1.0
O C:ASP674 4.9 25.3 1.0

Zinc binding site 4 out of 4 in 5sfo

Go back to Zinc Binding Sites List in 5sfo
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-[2-(1-Methyl-4-Phenylimidazol-2- Yl)Ethyl]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-[2-(1-Methyl-4-Phenylimidazol-2- Yl)Ethyl]Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:32.8
occ:1.00
 O D:HOH949 2.0 26.4 1.0
NE2 D:HIS529 2.2 29.4 1.0
NE2 D:HIS563 2.2 26.0 1.0
OD2 D:ASP564 2.2 30.9 1.0
OD1 D:ASP674 2.2 26.5 1.0
O D:HOH946 2.4 45.7 1.0
CD2 D:HIS563 3.0 27.4 1.0
CD2 D:HIS529 3.1 30.2 1.0
CG D:ASP674 3.1 29.7 1.0
CG D:ASP564 3.1 28.4 1.0
CE1 D:HIS529 3.2 28.4 1.0
CE1 D:HIS563 3.3 30.5 1.0
OD2 D:ASP674 3.3 34.1 1.0
OD1 D:ASP564 3.6 26.9 1.0
MG D:MG802 3.7 31.4 1.0
CD2 D:HIS525 4.1 32.7 1.0
O D:HOH966 4.2 27.3 1.0
CG D:HIS563 4.2 25.1 1.0
CG D:HIS529 4.2 28.6 1.0
O D:HOH945 4.3 34.5 1.0
ND1 D:HIS529 4.3 28.7 1.0
CB D:ASP564 4.3 28.0 1.0
ND1 D:HIS563 4.4 27.0 1.0
NE2 D:HIS525 4.4 34.3 1.0
CB D:ASP674 4.5 28.1 1.0
O D:HOH940 4.5 31.3 1.0
CG2 D:VAL533 4.7 31.9 1.0
O D:ASP674 4.8 30.5 1.0
CA D:ASP674 4.8 28.9 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 05:00:04 2024

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