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Zinc in PDB 5se8: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(2-Methyl-5-Phenyl-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-(2-Methyl-5-Phenyl-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-(2-Methyl-5-Phenyl-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-(2-Methyl-5-Phenyl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide, PDB code: 5se8 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) 43.69 / 1.99
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.812, 135.812, 235.994, 90, 90, 120
R / Rfree (%) 17.3 / 21.7

Other elements in 5se8:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(2-Methyl-5-Phenyl-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-(2-Methyl-5-Phenyl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide (pdb code 5se8). 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-(2-Methyl-5-Phenyl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide, PDB code: 5se8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5se8

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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-(2-Methyl-5-Phenyl-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-(2-Methyl-5-Phenyl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:28.7
occ:1.00
 OD2 A:ASP564 2.1 22.5 1.0
NE2 A:HIS529 2.1 24.8 1.0
O A:HOH980 2.2 21.7 1.0
NE2 A:HIS563 2.2 23.6 1.0
OD1 A:ASP674 2.2 27.8 1.0
O A:HOH1021 2.5 32.1 1.0
CD2 A:HIS563 3.0 22.5 1.0
CG A:ASP674 3.1 28.8 1.0
CD2 A:HIS529 3.1 26.3 1.0
CG A:ASP564 3.1 22.4 1.0
CE1 A:HIS529 3.2 24.3 1.0
OD2 A:ASP674 3.3 30.0 1.0
CE1 A:HIS563 3.3 26.8 1.0
OD1 A:ASP564 3.6 22.5 1.0
MG A:MG802 3.7 24.6 1.0
O A:HOH997 4.1 22.8 1.0
CD2 A:HIS525 4.2 30.2 1.0
CG A:HIS563 4.2 21.4 1.0
CG A:HIS529 4.3 23.4 1.0
ND1 A:HIS529 4.3 21.4 1.0
ND1 A:HIS563 4.3 25.3 1.0
O A:HOH999 4.4 30.7 1.0
CB A:ASP564 4.4 22.7 1.0
NE2 A:HIS525 4.5 28.3 1.0
CB A:ASP674 4.5 26.9 1.0
O A:HOH953 4.5 20.1 1.0
O A:HOH1030 4.6 50.6 1.0
CG2 A:VAL533 4.8 23.1 1.0
CA A:ASP674 4.9 23.6 1.0
O A:ASP674 4.9 22.7 1.0

Zinc binding site 2 out of 4 in 5se8

Go back to Zinc Binding Sites List in 5se8
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-(2-Methyl-5-Phenyl-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-(2-Methyl-5-Phenyl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:27.9
occ:1.00
 O B:HOH991 2.1 21.3 1.0
OD1 B:ASP674 2.2 20.7 1.0
NE2 B:HIS529 2.2 24.7 1.0
OD2 B:ASP564 2.2 20.7 1.0
NE2 B:HIS563 2.2 19.9 1.0
O B:HOH1004 2.4 35.0 1.0
CG B:ASP674 3.1 23.9 1.0
CD2 B:HIS563 3.1 20.4 1.0
CD2 B:HIS529 3.1 21.8 1.0
CG B:ASP564 3.2 21.3 1.0
CE1 B:HIS529 3.2 24.9 1.0
CE1 B:HIS563 3.3 21.5 1.0
OD2 B:ASP674 3.3 24.4 1.0
OD1 B:ASP564 3.6 22.7 1.0
MG B:MG802 3.8 23.0 1.0
CD2 B:HIS525 4.1 22.9 1.0
O B:HOH999 4.1 20.6 1.0
CG B:HIS563 4.3 21.7 1.0
CG B:HIS529 4.3 23.8 1.0
ND1 B:HIS529 4.3 23.6 1.0
O B:HOH936 4.3 28.1 1.0
ND1 B:HIS563 4.4 19.2 1.0
CB B:ASP564 4.4 20.6 1.0
NE2 B:HIS525 4.4 26.2 1.0
CB B:ASP674 4.4 25.1 1.0
O B:HOH943 4.6 21.9 1.0
CG2 B:VAL533 4.7 22.4 1.0
CA B:ASP674 4.9 23.9 1.0
O B:ASP674 4.9 23.0 1.0

Zinc binding site 3 out of 4 in 5se8

Go back to Zinc Binding Sites List in 5se8
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-(2-Methyl-5-Phenyl-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-(2-Methyl-5-Phenyl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:29.9
occ:1.00
 O C:HOH958 2.0 21.3 1.0
OD2 C:ASP564 2.2 26.5 1.0
NE2 C:HIS563 2.2 22.8 1.0
OD1 C:ASP674 2.2 24.8 1.0
NE2 C:HIS529 2.2 25.5 1.0
O C:HOH1016 2.3 31.1 1.0
CD2 C:HIS563 3.1 22.0 1.0
CG C:ASP674 3.1 25.9 1.0
CD2 C:HIS529 3.1 23.7 1.0
CG C:ASP564 3.2 23.4 1.0
CE1 C:HIS563 3.2 22.5 1.0
CE1 C:HIS529 3.3 27.5 1.0
OD2 C:ASP674 3.3 28.2 1.0
OD1 C:ASP564 3.6 21.7 1.0
MG C:MG802 3.7 24.0 1.0
CD2 C:HIS525 4.1 28.4 1.0
O C:HOH1036 4.2 24.8 1.0
CG C:HIS563 4.2 23.0 1.0
CG C:HIS529 4.3 25.2 1.0
ND1 C:HIS563 4.3 25.0 1.0
ND1 C:HIS529 4.3 23.8 1.0
O C:HOH994 4.4 31.5 1.0
CB C:ASP564 4.4 23.3 1.0
CB C:ASP674 4.4 24.3 1.0
NE2 C:HIS525 4.5 30.2 1.0
O C:HOH956 4.6 25.2 1.0
O C:HOH1048 4.6 43.0 1.0
CG2 C:VAL533 4.8 24.5 1.0
CA C:ASP674 4.8 26.9 1.0
O C:ASP674 4.9 26.7 1.0

Zinc binding site 4 out of 4 in 5se8

Go back to Zinc Binding Sites List in 5se8
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-(2-Methyl-5-Phenyl-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-(2-Methyl-5-Phenyl-1,2,4- Triazol-3-Yl)Ethyl]Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:33.9
occ:1.00
 O D:HOH960 2.0 24.6 1.0
OD2 D:ASP564 2.2 35.3 1.0
NE2 D:HIS529 2.2 31.9 1.0
NE2 D:HIS563 2.2 25.9 1.0
OD1 D:ASP674 2.2 29.5 1.0
O D:HOH949 2.4 41.4 1.0
CD2 D:HIS563 3.0 30.1 1.0
CD2 D:HIS529 3.1 34.5 1.0
CG D:ASP564 3.1 27.8 1.0
CG D:ASP674 3.1 31.1 1.0
CE1 D:HIS529 3.3 32.3 1.0
CE1 D:HIS563 3.3 30.0 1.0
OD2 D:ASP674 3.4 31.9 1.0
OD1 D:ASP564 3.6 29.1 1.0
MG D:MG802 3.7 31.8 1.0
CD2 D:HIS525 4.1 34.0 1.0
O D:HOH954 4.1 28.3 1.0
CG D:HIS563 4.2 28.1 1.0
O D:HOH927 4.3 35.8 1.0
CB D:ASP564 4.3 29.1 1.0
CG D:HIS529 4.3 28.7 1.0
ND1 D:HIS529 4.3 29.0 1.0
ND1 D:HIS563 4.4 29.2 1.0
NE2 D:HIS525 4.4 35.1 1.0
CB D:ASP674 4.5 29.1 1.0
O D:HOH928 4.5 28.9 1.0
CG2 D:VAL533 4.8 33.0 1.0
CA D:ASP674 4.9 27.4 1.0
O D:ASP674 4.9 31.0 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 04:37:42 2024

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