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Zinc in PDB 5sf8: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(5-Phenyl-2-Pyridin-2-Yl-1,2,4- Triazol-3-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-(5-Phenyl-2-Pyridin-2-Yl-1,2,4- Triazol-3-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-(5-Phenyl-2-Pyridin-2-Yl-1,2,4- Triazol-3-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-(5-Phenyl-2-Pyridin-2-Yl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide, PDB code: 5sf8 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) 43.49 / 2.15
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.206, 135.206, 235.361, 90, 90, 120
R / Rfree (%) 17.1 / 22.5

Other elements in 5sf8:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(5-Phenyl-2-Pyridin-2-Yl-1,2,4- Triazol-3-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-(5-Phenyl-2-Pyridin-2-Yl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide (pdb code 5sf8). 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-(5-Phenyl-2-Pyridin-2-Yl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide, PDB code: 5sf8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sf8

Go back to Zinc Binding Sites List in 5sf8
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-(5-Phenyl-2-Pyridin-2-Yl-1,2,4- Triazol-3-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-(5-Phenyl-2-Pyridin-2-Yl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:35.2
occ:1.00
 NE2 A:HIS563 2.1 27.0 1.0
OD2 A:ASP564 2.2 31.9 1.0
NE2 A:HIS529 2.2 33.4 1.0
OD1 A:ASP674 2.2 28.7 1.0
O A:HOH994 2.2 29.3 1.0
O A:HOH1008 2.4 36.3 1.0
CD2 A:HIS563 3.0 27.3 1.0
CG A:ASP674 3.1 31.1 1.0
CG A:ASP564 3.1 30.2 1.0
CD2 A:HIS529 3.1 30.7 1.0
CE1 A:HIS529 3.2 34.4 1.0
CE1 A:HIS563 3.2 31.4 1.0
OD2 A:ASP674 3.4 34.8 1.0
OD1 A:ASP564 3.6 29.4 1.0
MG A:MG802 3.7 28.5 1.0
CD2 A:HIS525 4.1 34.7 1.0
CG A:HIS563 4.2 26.8 1.0
O A:HOH1002 4.2 30.1 1.0
ND1 A:HIS563 4.3 28.4 1.0
CG A:HIS529 4.3 29.2 1.0
ND1 A:HIS529 4.3 31.0 1.0
CB A:ASP564 4.3 27.7 1.0
O A:HOH959 4.3 33.3 1.0
CB A:ASP674 4.4 28.5 1.0
NE2 A:HIS525 4.5 34.0 1.0
O A:HOH912 4.5 22.3 1.0
CG2 A:VAL533 4.7 25.9 1.0
O A:HOH1016 4.8 48.9 1.0
O A:ASP674 4.8 28.6 1.0
CA A:ASP674 4.8 28.4 1.0

Zinc binding site 2 out of 4 in 5sf8

Go back to Zinc Binding Sites List in 5sf8
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-(5-Phenyl-2-Pyridin-2-Yl-1,2,4- Triazol-3-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-(5-Phenyl-2-Pyridin-2-Yl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:32.9
occ:1.00
 O B:HOH982 2.1 23.1 1.0
NE2 B:HIS563 2.2 26.6 1.0
OD1 B:ASP674 2.2 29.4 1.0
NE2 B:HIS529 2.2 21.6 1.0
OD2 B:ASP564 2.2 25.5 1.0
O B:HOH976 2.6 37.2 1.0
CD2 B:HIS563 3.0 28.2 1.0
CG B:ASP674 3.0 27.1 1.0
CD2 B:HIS529 3.1 26.4 1.0
CG B:ASP564 3.1 26.2 1.0
CE1 B:HIS563 3.3 27.0 1.0
OD2 B:ASP674 3.3 30.3 1.0
CE1 B:HIS529 3.3 25.4 1.0
OD1 B:ASP564 3.5 25.8 1.0
MG B:MG802 3.7 28.4 1.0
O B:HOH1003 4.1 23.4 1.0
CD2 B:HIS525 4.1 29.7 1.0
CG B:HIS563 4.2 26.0 1.0
O B:HOH947 4.3 34.0 1.0
CG B:HIS529 4.3 26.2 1.0
ND1 B:HIS563 4.3 24.7 1.0
CB B:ASP564 4.3 27.1 1.0
ND1 B:HIS529 4.4 24.2 1.0
NE2 B:HIS525 4.4 30.4 1.0
CB B:ASP674 4.4 27.2 1.0
O B:HOH953 4.5 28.8 1.0
O B:HOH1041 4.7 55.6 1.0
CG2 B:VAL533 4.7 24.1 1.0
CA B:ASP674 4.8 26.2 1.0
O B:ASP674 4.8 28.2 1.0

Zinc binding site 3 out of 4 in 5sf8

Go back to Zinc Binding Sites List in 5sf8
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-(5-Phenyl-2-Pyridin-2-Yl-1,2,4- Triazol-3-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-(5-Phenyl-2-Pyridin-2-Yl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:34.0
occ:1.00
 O C:HOH968 2.0 23.3 1.0
OD1 C:ASP674 2.2 30.3 1.0
OD2 C:ASP564 2.2 31.1 1.0
NE2 C:HIS563 2.2 26.4 1.0
NE2 C:HIS529 2.2 30.7 1.0
O C:HOH1017 2.4 33.5 1.0
CG C:ASP674 3.0 27.8 1.0
CD2 C:HIS563 3.0 25.9 1.0
OD2 C:ASP674 3.1 28.8 1.0
CG C:ASP564 3.2 27.2 1.0
CD2 C:HIS529 3.2 31.8 1.0
CE1 C:HIS529 3.2 33.3 1.0
CE1 C:HIS563 3.3 29.1 1.0
OD1 C:ASP564 3.6 26.6 1.0
MG C:MG802 3.8 26.2 1.0
CD2 C:HIS525 4.1 31.8 1.0
O C:HOH1008 4.2 27.4 1.0
CG C:HIS563 4.2 26.2 1.0
O C:HOH990 4.3 29.2 1.0
CG C:HIS529 4.3 30.9 1.0
ND1 C:HIS529 4.3 30.8 1.0
ND1 C:HIS563 4.4 29.0 1.0
CB C:ASP674 4.4 29.7 1.0
CB C:ASP564 4.4 26.1 1.0
NE2 C:HIS525 4.4 34.5 1.0
O C:HOH936 4.6 26.1 1.0
O C:HOH1035 4.7 44.7 1.0
CA C:ASP674 4.8 31.7 1.0
CG2 C:VAL533 4.8 29.0 1.0
O C:ASP674 4.9 32.6 1.0

Zinc binding site 4 out of 4 in 5sf8

Go back to Zinc Binding Sites List in 5sf8
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-(5-Phenyl-2-Pyridin-2-Yl-1,2,4- Triazol-3-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-(5-Phenyl-2-Pyridin-2-Yl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:44.1
occ:1.00
 O D:HOH956 2.1 29.4 1.0
OD2 D:ASP564 2.1 44.7 1.0
NE2 D:HIS563 2.2 34.4 1.0
NE2 D:HIS529 2.2 37.3 1.0
OD1 D:ASP674 2.3 46.1 1.0
O D:HOH935 2.4 44.2 1.0
CD2 D:HIS563 3.0 32.9 1.0
CG D:ASP674 3.1 40.3 1.0
CD2 D:HIS529 3.1 41.3 1.0
CG D:ASP564 3.2 36.9 1.0
CE1 D:HIS529 3.3 40.5 1.0
OD2 D:ASP674 3.3 41.8 1.0
CE1 D:HIS563 3.4 38.5 1.0
OD1 D:ASP564 3.7 34.9 1.0
MG D:MG802 3.9 37.8 1.0
CD2 D:HIS525 4.1 40.2 1.0
O D:HOH936 4.1 32.8 1.0
CG D:HIS563 4.2 34.4 1.0
CG D:HIS529 4.3 36.7 1.0
CB D:ASP564 4.3 36.9 1.0
O D:HOH930 4.3 42.4 1.0
ND1 D:HIS563 4.4 36.3 1.0
ND1 D:HIS529 4.4 39.6 1.0
NE2 D:HIS525 4.4 44.5 1.0
O D:HOH914 4.4 36.8 1.0
CB D:ASP674 4.5 41.4 1.0
CG2 D:VAL533 4.7 42.8 1.0
CA D:ASP674 4.9 40.4 1.0
O D:ASP674 4.9 43.3 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 04:51:34 2024

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