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Zinc in PDB 5sdv: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-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 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide, PDB code: 5sdv 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) 43.73 / 2.15
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.343, 135.343, 235.651, 90, 90, 120
R / Rfree (%) 17.5 / 23.2

Other elements in 5sdv:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide 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 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide (pdb code 5sdv). 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 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide, PDB code: 5sdv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sdv

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-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 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:27.4
occ:1.00
 OD2 A:ASP564 2.1 26.9 1.0
NE2 A:HIS563 2.1 22.1 1.0
NE2 A:HIS529 2.2 25.9 1.0
OD1 A:ASP674 2.2 31.0 1.0
O A:HOH956 2.2 25.9 1.0
O A:HOH994 2.3 27.8 1.0
CD2 A:HIS563 3.0 19.8 1.0
CG A:ASP674 3.0 29.1 1.0
CG A:ASP564 3.1 24.8 1.0
CD2 A:HIS529 3.1 23.4 1.0
CE1 A:HIS529 3.2 25.7 1.0
OD2 A:ASP674 3.2 38.8 1.0
CE1 A:HIS563 3.2 25.0 1.0
OD1 A:ASP564 3.6 23.1 1.0
MG A:MG802 3.8 23.4 1.0
CG A:HIS563 4.2 25.5 1.0
O A:HOH1020 4.2 23.0 1.0
CD2 A:HIS525 4.2 29.2 1.0
ND1 A:HIS563 4.3 24.5 1.0
CB A:ASP564 4.3 21.3 1.0
ND1 A:HIS529 4.3 23.9 1.0
CG A:HIS529 4.3 27.0 1.0
O A:HOH946 4.3 34.2 1.0
CB A:ASP674 4.4 23.3 1.0
O A:HOH1019 4.5 46.9 1.0
NE2 A:HIS525 4.5 25.7 1.0
O A:HOH950 4.6 19.7 1.0
CG2 A:VAL533 4.7 19.0 1.0
O A:ASP674 4.8 23.9 1.0
CA A:ASP674 4.8 21.7 1.0

Zinc binding site 2 out of 4 in 5sdv

Go back to Zinc Binding Sites List in 5sdv
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-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 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:25.3
occ:1.00
 OD1 B:ASP674 2.1 28.1 1.0
OD2 B:ASP564 2.1 20.5 1.0
NE2 B:HIS563 2.1 18.3 1.0
O B:HOH946 2.1 16.6 1.0
NE2 B:HIS529 2.1 19.3 1.0
O B:HOH990 2.3 27.7 1.0
CG B:ASP674 3.0 26.0 1.0
CD2 B:HIS563 3.1 22.1 1.0
CD2 B:HIS529 3.1 22.7 1.0
CG B:ASP564 3.2 19.9 1.0
OD2 B:ASP674 3.2 31.7 1.0
CE1 B:HIS563 3.2 23.3 1.0
CE1 B:HIS529 3.2 23.1 1.0
OD1 B:ASP564 3.6 22.1 1.0
MG B:MG802 3.8 22.7 1.0
O B:HOH1021 4.0 23.1 1.0
CD2 B:HIS525 4.1 24.7 1.0
CG B:HIS563 4.2 20.7 1.0
CG B:HIS529 4.2 22.3 1.0
ND1 B:HIS563 4.3 17.6 1.0
ND1 B:HIS529 4.3 20.9 1.0
CB B:ASP564 4.3 19.7 1.0
O B:HOH989 4.4 31.6 1.0
CB B:ASP674 4.4 22.5 1.0
NE2 B:HIS525 4.4 24.9 1.0
O B:HOH931 4.6 17.5 1.0
CA B:ASP674 4.8 24.3 1.0
CG2 B:VAL533 4.8 19.4 1.0
O B:ASP674 4.8 22.8 1.0

Zinc binding site 3 out of 4 in 5sdv

Go back to Zinc Binding Sites List in 5sdv
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-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 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:30.2
occ:1.00
 O C:HOH986 2.1 21.4 1.0
NE2 C:HIS529 2.1 21.2 1.0
OD1 C:ASP674 2.2 26.2 1.0
OD2 C:ASP564 2.2 27.2 1.0
NE2 C:HIS563 2.2 19.1 1.0
O C:HOH987 2.3 30.6 1.0
CD2 C:HIS529 3.0 25.1 1.0
CD2 C:HIS563 3.1 21.6 1.0
CG C:ASP674 3.1 28.9 1.0
CG C:ASP564 3.1 27.3 1.0
CE1 C:HIS529 3.2 27.2 1.0
CE1 C:HIS563 3.3 21.3 1.0
OD2 C:ASP674 3.4 36.5 1.0
OD1 C:ASP564 3.6 23.1 1.0
MG C:MG802 3.8 22.7 1.0
CD2 C:HIS525 4.0 32.1 1.0
O C:HOH1027 4.2 20.7 1.0
CG C:HIS529 4.2 24.2 1.0
CG C:HIS563 4.2 23.3 1.0
ND1 C:HIS529 4.3 22.3 1.0
ND1 C:HIS563 4.3 21.1 1.0
CB C:ASP564 4.3 22.3 1.0
NE2 C:HIS525 4.3 29.4 1.0
O C:HOH980 4.4 38.1 1.0
CB C:ASP674 4.4 26.4 1.0
O C:HOH947 4.6 24.6 1.0
CG2 C:VAL533 4.8 23.7 1.0
CA C:ASP674 4.8 24.8 1.0
O C:ASP674 4.9 28.6 1.0

Zinc binding site 4 out of 4 in 5sdv

Go back to Zinc Binding Sites List in 5sdv
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-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 2- Methyl-4-N-(1,3-Oxazol-4-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:37.0
occ:1.00
 NE2 D:HIS563 2.1 23.5 1.0
O D:HOH922 2.1 22.3 1.0
NE2 D:HIS529 2.2 31.3 1.0
OD2 D:ASP564 2.3 38.6 1.0
O D:HOH945 2.3 34.3 1.0
OD1 D:ASP674 2.3 33.6 1.0
CD2 D:HIS563 2.9 28.2 1.0
CG D:ASP674 3.0 33.5 1.0
CD2 D:HIS529 3.1 36.7 1.0
CG D:ASP564 3.2 28.8 1.0
OD2 D:ASP674 3.2 33.8 1.0
CE1 D:HIS529 3.2 31.6 1.0
CE1 D:HIS563 3.2 28.6 1.0
OD1 D:ASP564 3.7 31.9 1.0
MG D:MG802 3.9 32.8 1.0
CG D:HIS563 4.1 27.5 1.0
CD2 D:HIS525 4.2 37.5 1.0
O D:HOH947 4.2 36.9 1.0
ND1 D:HIS563 4.2 29.3 1.0
O D:HOH981 4.3 32.7 1.0
CB D:ASP564 4.3 29.8 1.0
ND1 D:HIS529 4.3 32.0 1.0
CG D:HIS529 4.3 31.4 1.0
CB D:ASP674 4.4 31.2 1.0
O D:HOH935 4.4 31.1 1.0
NE2 D:HIS525 4.5 39.3 1.0
O D:ASP674 4.7 30.9 1.0
CG2 D:VAL533 4.7 32.7 1.0
CA D:ASP674 4.8 30.1 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 04:30:07 2024

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