Zinc in PDB 5ser: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide, PDB code: 5ser was solved by C.Joseph, A.Flohr, 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 / 2.25
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.109, 135.109, 234.956, 90, 90, 120
R / Rfree (%) 17.2 / 23.3

Other elements in 5ser:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide also contains other interesting chemical elements:

Fluorine (F) 4 atoms
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-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide (pdb code 5ser). 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-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide, PDB code: 5ser:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5ser

Go back to Zinc Binding Sites List in 5ser
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide


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-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:42.2
occ:1.00
 OD2 A:ASP564 2.1 36.5 1.0
O A:HOH941 2.1 30.9 1.0
O A:HOH956 2.1 35.4 1.0
NE2 A:HIS529 2.1 41.5 1.0
NE2 A:HIS563 2.1 34.9 1.0
OD1 A:ASP674 2.2 41.8 1.0
CD2 A:HIS563 3.0 32.0 1.0
CD2 A:HIS529 3.1 38.1 1.0
CG A:ASP674 3.1 37.4 1.0
CG A:ASP564 3.1 33.8 1.0
CE1 A:HIS529 3.1 37.6 1.0
CE1 A:HIS563 3.2 42.2 1.0
OD2 A:ASP674 3.3 38.7 1.0
OD1 A:ASP564 3.6 35.0 1.0
MG A:MG802 3.8 34.2 1.0
O A:HOH967 4.1 28.5 1.0
O A:HOH936 4.1 43.2 1.0
CG A:HIS563 4.2 36.7 1.0
CD2 A:HIS525 4.2 35.0 1.0
ND1 A:HIS563 4.2 37.6 1.0
ND1 A:HIS529 4.2 39.9 1.0
CG A:HIS529 4.3 35.8 1.0
CB A:ASP564 4.3 31.3 1.0
NE2 A:HIS525 4.4 41.0 1.0
CB A:ASP674 4.4 37.5 1.0
O A:HOH977 4.5 60.0 1.0
O A:HOH916 4.6 29.0 1.0
CG2 A:VAL533 4.8 28.7 1.0
CA A:ASP674 4.9 37.1 1.0
O A:ASP674 4.9 35.8 1.0

Zinc binding site 2 out of 4 in 5ser

Go back to Zinc Binding Sites List in 5ser
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide


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-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:40.8
occ:1.00
 O B:HOH955 1.9 27.7 1.0
OD2 B:ASP564 2.1 34.7 1.0
NE2 B:HIS563 2.2 33.2 1.0
NE2 B:HIS529 2.2 28.6 1.0
OD1 B:ASP674 2.2 33.0 1.0
O B:HOH956 2.6 41.0 1.0
CD2 B:HIS563 3.1 38.5 1.0
CG B:ASP674 3.1 31.2 1.0
CG B:ASP564 3.1 33.4 1.0
CD2 B:HIS529 3.1 37.6 1.0
CE1 B:HIS563 3.2 31.2 1.0
CE1 B:HIS529 3.2 37.5 1.0
OD2 B:ASP674 3.4 34.5 1.0
OD1 B:ASP564 3.5 32.7 1.0
MG B:MG802 3.7 32.0 1.0
O B:HOH970 3.9 27.6 1.0
CD2 B:HIS525 4.1 37.9 1.0
O B:HOH907 4.1 37.9 1.0
CG B:HIS563 4.2 32.8 1.0
ND1 B:HIS563 4.3 31.6 1.0
CG B:HIS529 4.3 33.2 1.0
ND1 B:HIS529 4.3 34.9 1.0
CB B:ASP564 4.3 32.5 1.0
O B:HOH984 4.4 60.6 1.0
NE2 B:HIS525 4.5 36.7 1.0
CB B:ASP674 4.5 31.6 1.0
CG2 B:VAL533 4.7 29.6 1.0
O B:HOH927 4.8 35.3 1.0
O B:ASP674 4.8 34.2 1.0
CA B:ASP674 4.9 30.0 1.0

Zinc binding site 3 out of 4 in 5ser

Go back to Zinc Binding Sites List in 5ser
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide


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-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:40.2
occ:1.00
 O C:HOH929 1.9 29.6 1.0
OD2 C:ASP564 2.2 36.4 1.0
OD1 C:ASP674 2.2 36.8 1.0
NE2 C:HIS529 2.2 36.2 1.0
NE2 C:HIS563 2.3 33.1 1.0
O C:HOH951 2.3 42.6 1.0
CG C:ASP674 3.1 35.6 1.0
CD2 C:HIS563 3.1 32.1 1.0
CG C:ASP564 3.1 32.4 1.0
CE1 C:HIS529 3.2 37.1 1.0
CD2 C:HIS529 3.2 39.3 1.0
OD2 C:ASP674 3.3 37.0 1.0
CE1 C:HIS563 3.4 34.0 1.0
OD1 C:ASP564 3.6 33.4 1.0
MG C:MG802 3.7 33.6 1.0
CD2 C:HIS525 4.1 40.4 1.0
O C:HOH978 4.2 33.9 1.0
ND1 C:HIS529 4.3 34.6 1.0
CG C:HIS563 4.3 34.5 1.0
CG C:HIS529 4.3 35.7 1.0
CB C:ASP564 4.3 26.6 1.0
O C:HOH936 4.3 40.7 1.0
NE2 C:HIS525 4.4 42.3 1.0
ND1 C:HIS563 4.4 32.9 1.0
CB C:ASP674 4.5 33.9 1.0
O C:HOH981 4.5 49.7 1.0
O C:HOH928 4.5 35.3 1.0
CA C:ASP674 4.8 37.4 1.0
CG2 C:VAL533 4.8 33.1 1.0
O C:HOH942 4.9 35.4 1.0
O C:ASP674 5.0 37.8 1.0

Zinc binding site 4 out of 4 in 5ser

Go back to Zinc Binding Sites List in 5ser
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide


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-N- (2-Fluoroethyl)-4-N,2-Dimethyl-3-N-(2-Phenyl-[1,2,4]Triazolo[1,5- A]Pyridin-7-Yl)Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:56.5
occ:1.00
 OD2 D:ASP564 2.1 61.4 1.0
NE2 D:HIS563 2.2 44.1 1.0
OD1 D:ASP674 2.2 67.6 1.0
O D:HOH911 2.2 34.9 1.0
NE2 D:HIS529 2.2 50.3 1.0
O D:HOH924 2.3 45.6 1.0
CD2 D:HIS563 3.0 53.5 1.0
CG D:ASP564 3.1 50.8 1.0
CG D:ASP674 3.2 51.1 1.0
CD2 D:HIS529 3.2 55.3 1.0
CE1 D:HIS529 3.2 52.3 1.0
CE1 D:HIS563 3.2 42.8 1.0
OD2 D:ASP674 3.4 55.2 1.0
OD1 D:ASP564 3.6 52.3 1.0
O D:HOH908 3.9 43.0 1.0
MG D:MG802 4.0 48.7 1.0
CB D:ASP564 4.2 44.7 1.0
CG D:HIS563 4.2 50.9 1.0
CD2 D:HIS525 4.3 68.7 1.0
ND1 D:HIS563 4.3 52.5 1.0
ND1 D:HIS529 4.3 55.2 1.0
CG D:HIS529 4.4 51.3 1.0
CB D:ASP674 4.5 55.2 1.0
NE2 D:HIS525 4.6 61.4 1.0
O D:HOH903 4.6 47.9 1.0
CG2 D:VAL533 4.7 53.7 1.0
O D:ASP674 4.9 62.5 1.0
CA D:ASP674 5.0 55.6 1.0
O D:HOH902 5.0 48.2 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 04:46:48 2024

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