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Zinc in PDB 5sfq: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-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)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide, PDB code: 5sfq 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) 43.26 / 2.21
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.458, 134.458, 234.587, 90, 90, 120
R / Rfree (%) 18.6 / 24.8

Other elements in 5sfq:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Fluorine (F) 8 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)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide (pdb code 5sfq). 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)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide, PDB code: 5sfq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sfq

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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)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-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)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:28.0
occ:1.00
 OD2 A:ASP564 2.1 24.3 1.0
NE2 A:HIS563 2.1 19.5 1.0
O A:HOH926 2.1 18.3 1.0
NE2 A:HIS529 2.1 26.1 1.0
OD1 A:ASP674 2.1 24.6 1.0
O A:HOH989 2.3 20.8 1.0
CG A:ASP674 3.0 26.4 1.0
CD2 A:HIS563 3.0 20.8 1.0
CE1 A:HIS529 3.1 25.4 1.0
CG A:ASP564 3.1 22.5 1.0
CE1 A:HIS563 3.1 23.1 1.0
CD2 A:HIS529 3.1 24.4 1.0
OD2 A:ASP674 3.2 36.0 1.0
OD1 A:ASP564 3.6 23.5 1.0
MG A:MG802 3.8 22.2 1.0
O A:HOH1002 4.1 18.6 1.0
CG A:HIS563 4.2 21.9 1.0
ND1 A:HIS529 4.2 23.8 1.0
ND1 A:HIS563 4.2 21.7 1.0
CG A:HIS529 4.2 23.2 1.0
CB A:ASP564 4.2 20.1 1.0
CD2 A:HIS525 4.2 28.0 1.0
O A:HOH945 4.3 29.3 1.0
CB A:ASP674 4.4 23.6 1.0
NE2 A:HIS525 4.4 24.4 1.0
O A:HOH956 4.6 22.2 1.0
CG2 A:VAL533 4.7 23.2 1.0
O A:HOH1027 4.8 41.0 1.0
CA A:ASP674 4.8 22.6 1.0
O A:ASP674 4.9 23.3 1.0

Zinc binding site 2 out of 4 in 5sfq

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-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)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:26.0
occ:1.00
 NE2 B:HIS563 2.0 17.3 1.0
O B:HOH931 2.1 12.7 1.0
OD2 B:ASP564 2.1 20.6 1.0
OD1 B:ASP674 2.1 22.2 1.0
NE2 B:HIS529 2.2 22.4 1.0
O B:HOH956 2.4 27.5 1.0
CD2 B:HIS563 3.0 18.3 1.0
CG B:ASP674 3.0 23.3 1.0
CG B:ASP564 3.1 22.5 1.0
CE1 B:HIS563 3.1 19.9 1.0
CE1 B:HIS529 3.2 25.7 1.0
CD2 B:HIS529 3.2 24.8 1.0
OD2 B:ASP674 3.2 22.9 1.0
OD1 B:ASP564 3.5 21.6 1.0
MG B:MG802 3.8 21.4 1.0
O B:HOH974 4.1 17.2 1.0
CG B:HIS563 4.1 18.3 1.0
CD2 B:HIS525 4.1 24.3 1.0
ND1 B:HIS563 4.2 18.2 1.0
ND1 B:HIS529 4.3 23.0 1.0
CG B:HIS529 4.3 24.4 1.0
CB B:ASP564 4.3 21.9 1.0
O B:HOH987 4.3 25.3 1.0
NE2 B:HIS525 4.3 23.6 1.0
CB B:ASP674 4.4 22.7 1.0
O B:HOH1043 4.5 49.2 1.0
O B:HOH939 4.6 21.0 1.0
CG2 B:VAL533 4.7 20.7 1.0
CA B:ASP674 4.8 22.1 1.0
O B:ASP674 5.0 24.7 1.0

Zinc binding site 3 out of 4 in 5sfq

Go back to Zinc Binding Sites List in 5sfq
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-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)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:31.9
occ:1.00
 NE2 C:HIS563 1.9 21.5 1.0
O C:HOH987 2.1 34.2 1.0
O C:HOH922 2.2 21.7 1.0
OD1 C:ASP674 2.2 28.2 1.0
NE2 C:HIS529 2.2 26.5 1.0
OD2 C:ASP564 2.3 21.3 1.0
CD2 C:HIS563 2.9 22.6 1.0
CE1 C:HIS563 3.0 23.3 1.0
CG C:ASP674 3.0 27.5 1.0
CE1 C:HIS529 3.2 28.9 1.0
CG C:ASP564 3.2 23.6 1.0
CD2 C:HIS529 3.2 27.6 1.0
OD2 C:ASP674 3.2 29.3 1.0
OD1 C:ASP564 3.6 25.0 1.0
MG C:MG802 3.9 27.2 1.0
CG C:HIS563 4.1 24.3 1.0
ND1 C:HIS563 4.1 21.1 1.0
CD2 C:HIS525 4.2 33.6 1.0
ND1 C:HIS529 4.3 26.9 1.0
O C:HOH996 4.3 21.4 1.0
CG C:HIS529 4.3 28.5 1.0
CB C:ASP674 4.3 29.5 1.0
O C:HOH923 4.3 24.1 1.0
CB C:ASP564 4.4 22.2 1.0
NE2 C:HIS525 4.4 33.8 1.0
O C:HOH988 4.4 30.6 1.0
O C:HOH1029 4.6 44.2 1.0
CA C:ASP674 4.8 28.7 1.0
CG2 C:VAL533 4.8 23.6 1.0
O C:ASP674 4.9 27.1 1.0

Zinc binding site 4 out of 4 in 5sfq

Go back to Zinc Binding Sites List in 5sfq
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-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)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:32.0
occ:1.00
 NE2 D:HIS563 2.1 25.6 1.0
O D:HOH935 2.1 21.0 1.0
NE2 D:HIS529 2.2 30.1 1.0
O D:HOH988 2.2 25.1 1.0
OD1 D:ASP674 2.2 24.1 1.0
OD2 D:ASP564 2.2 30.0 1.0
CD2 D:HIS563 3.0 23.9 1.0
CG D:ASP674 3.1 24.8 1.0
CG D:ASP564 3.1 26.6 1.0
CD2 D:HIS529 3.1 33.0 1.0
CE1 D:HIS563 3.2 28.1 1.0
OD2 D:ASP674 3.3 27.7 1.0
CE1 D:HIS529 3.3 34.5 1.0
OD1 D:ASP564 3.5 28.4 1.0
MG D:MG802 3.8 26.5 1.0
CG D:HIS563 4.1 24.3 1.0
CD2 D:HIS525 4.2 32.3 1.0
ND1 D:HIS563 4.2 25.0 1.0
CB D:ASP564 4.3 24.2 1.0
O D:HOH939 4.3 30.5 1.0
CG D:HIS529 4.3 32.2 1.0
ND1 D:HIS529 4.4 32.1 1.0
O D:HOH960 4.4 24.0 1.0
CB D:ASP674 4.5 24.0 1.0
O D:HOH932 4.5 21.8 1.0
NE2 D:HIS525 4.5 33.5 1.0
O D:ASP674 4.8 29.1 1.0
CG2 D:VAL533 4.8 32.8 1.0
CA D:ASP674 4.9 25.1 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 05:02:03 2024

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