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

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

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)-4-N-(Pyridin-2- Ylmethyl)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-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)-4-N-(Pyridin-2- Ylmethyl)Pyrazole-3,4-Dicarboxamide, PDB code: 5sfj 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) 43.65 / 2.41
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.771, 134.771, 235.33, 90, 90, 120
R / Rfree (%) 18.6 / 24.5

Other elements in 5sfj:

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

Zinc binding site 1 out of 4 in 5sfj

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

b:42.1
occ:1.00
 OD2 A:ASP564 2.0 34.0 1.0
O A:HOH948 2.0 42.6 1.0
NE2 A:HIS563 2.1 32.6 1.0
NE2 A:HIS529 2.1 34.7 1.0
OD1 A:ASP674 2.1 42.2 1.0
O A:HOH936 2.3 34.9 1.0
CD2 A:HIS563 3.0 35.1 1.0
CG A:ASP674 3.0 41.7 1.0
CE1 A:HIS563 3.1 35.4 1.0
CE1 A:HIS529 3.1 36.1 1.0
CG A:ASP564 3.1 31.9 1.0
CD2 A:HIS529 3.1 34.9 1.0
OD2 A:ASP674 3.3 44.1 1.0
OD1 A:ASP564 3.7 30.0 1.0
MG A:MG802 3.7 30.5 1.0
CD2 A:HIS525 4.1 39.8 1.0
CG A:HIS563 4.2 36.1 1.0
ND1 A:HIS563 4.2 33.3 1.0
ND1 A:HIS529 4.2 36.9 1.0
CB A:ASP564 4.2 31.3 1.0
CG A:HIS529 4.3 32.3 1.0
O A:HOH956 4.3 27.1 1.0
NE2 A:HIS525 4.4 38.9 1.0
CB A:ASP674 4.4 37.1 1.0
O A:ASP674 4.6 37.1 1.0
O A:HOH912 4.7 25.1 1.0
CG2 A:VAL533 4.7 29.8 1.0
CA A:ASP674 4.8 34.7 1.0

Zinc binding site 2 out of 4 in 5sfj

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

b:36.1
occ:1.00
 NE2 B:HIS563 2.1 30.7 1.0
OD2 B:ASP564 2.1 38.4 1.0
OD1 B:ASP674 2.2 31.4 1.0
O B:HOH927 2.2 22.9 1.0
NE2 B:HIS529 2.2 29.8 1.0
O B:HOH963 2.5 35.6 1.0
CD2 B:HIS563 3.0 31.3 1.0
CG B:ASP564 3.0 31.0 1.0
CG B:ASP674 3.0 32.9 1.0
CD2 B:HIS529 3.1 31.6 1.0
CE1 B:HIS563 3.1 34.1 1.0
CE1 B:HIS529 3.2 30.3 1.0
OD2 B:ASP674 3.3 37.6 1.0
OD1 B:ASP564 3.4 31.7 1.0
MG B:MG802 3.7 30.7 1.0
O B:HOH968 3.9 22.8 1.0
CG B:HIS563 4.1 29.8 1.0
ND1 B:HIS563 4.2 33.4 1.0
ND1 B:HIS529 4.3 32.9 1.0
CB B:ASP564 4.3 30.7 1.0
CG B:HIS529 4.3 31.4 1.0
CD2 B:HIS525 4.3 37.4 1.0
CB B:ASP674 4.4 31.1 1.0
O B:HOH958 4.5 32.6 1.0
O B:HOH923 4.6 30.3 1.0
NE2 B:HIS525 4.6 29.1 1.0
O B:ASP674 4.8 32.6 1.0
CG2 B:VAL533 4.8 29.1 1.0
CA B:ASP674 4.9 29.3 1.0

Zinc binding site 3 out of 4 in 5sfj

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

b:42.6
occ:1.00
 OD1 C:ASP674 2.0 34.1 1.0
OD2 C:ASP564 2.1 33.5 1.0
NE2 C:HIS563 2.1 31.9 1.0
NE2 C:HIS529 2.2 33.8 1.0
O C:HOH907 2.2 29.1 1.0
CG C:ASP674 2.9 32.9 1.0
CD2 C:HIS563 3.1 30.4 1.0
OD2 C:ASP674 3.1 32.4 1.0
CE1 C:HIS563 3.2 33.4 1.0
CE1 C:HIS529 3.2 32.5 1.0
CG C:ASP564 3.2 31.7 1.0
CD2 C:HIS529 3.2 33.4 1.0
MG C:MG802 3.7 30.0 1.0
OD1 C:ASP564 3.7 31.5 1.0
CD2 C:HIS525 4.0 47.1 1.0
CG C:HIS563 4.3 31.8 1.0
O C:HOH961 4.3 30.0 1.0
ND1 C:HIS563 4.3 30.0 1.0
NE2 C:HIS525 4.3 50.1 1.0
ND1 C:HIS529 4.3 31.8 1.0
CB C:ASP674 4.3 37.1 1.0
CG C:HIS529 4.3 35.1 1.0
CB C:ASP564 4.4 27.8 1.0
O C:HOH931 4.5 37.1 1.0
CA C:ASP674 4.8 36.1 1.0
O C:ASP674 4.8 41.8 1.0
CG2 C:VAL533 4.9 35.6 1.0

Zinc binding site 4 out of 4 in 5sfj

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

b:56.4
occ:1.00
 O D:HOH902 1.9 38.8 1.0
NE2 D:HIS563 2.1 41.3 1.0
OD1 D:ASP674 2.1 45.0 1.0
OD2 D:ASP564 2.1 58.2 1.0
NE2 D:HIS529 2.3 51.4 1.0
O D:HOH914 2.4 41.2 1.0
CD2 D:HIS563 2.9 42.4 1.0
CG D:ASP674 3.0 45.6 1.0
CD2 D:HIS529 3.1 57.4 1.0
CG D:ASP564 3.1 52.9 1.0
OD2 D:ASP674 3.1 46.7 1.0
CE1 D:HIS563 3.2 41.4 1.0
CE1 D:HIS529 3.4 47.4 1.0
MG D:MG802 3.6 46.9 1.0
OD1 D:ASP564 3.7 50.4 1.0
O D:HOH915 3.9 51.3 1.0
CG D:HIS563 4.1 42.5 1.0
ND1 D:HIS563 4.2 39.2 1.0
CB D:ASP564 4.2 50.0 1.0
CD2 D:HIS525 4.2 54.6 1.0
CG D:HIS529 4.3 50.0 1.0
CB D:ASP674 4.4 47.2 1.0
ND1 D:HIS529 4.4 51.6 1.0
O D:HOH912 4.4 35.7 1.0
NE2 D:HIS525 4.7 53.5 1.0
CG2 D:VAL533 4.8 57.4 1.0
CA D:ASP674 4.8 48.1 1.0
O D:ASP674 4.9 61.9 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 04:58:09 2024

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