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Zinc in PDB 5sf7: Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One, PDB code: 5sf7 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) 43.52 / 2.08
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.284, 135.284, 235.352, 90, 90, 120
R / Rfree (%) 18.2 / 22.9

Other elements in 5sf7:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One also contains other interesting chemical elements:

Chlorine (Cl) 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 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One (pdb code 5sf7). 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 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One, PDB code: 5sf7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sf7

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One


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 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:28.6
occ:1.00
 OD2 A:ASP564 2.0 23.3 1.0
NE2 A:HIS563 2.1 25.8 1.0
NE2 A:HIS529 2.1 28.4 1.0
O A:HOH1001 2.2 22.8 1.0
OD1 A:ASP674 2.2 27.1 1.0
O A:HOH939 2.3 29.4 1.0
CD2 A:HIS563 3.0 24.1 1.0
CE1 A:HIS563 3.1 26.1 1.0
CG A:ASP564 3.1 23.6 1.0
CD2 A:HIS529 3.1 26.0 1.0
CG A:ASP674 3.1 28.3 1.0
CE1 A:HIS529 3.1 27.0 1.0
OD2 A:ASP674 3.3 31.4 1.0
OD1 A:ASP564 3.6 23.1 1.0
MG A:MG802 3.9 23.8 1.0
O A:HOH938 4.1 22.5 1.0
O A:HOH999 4.1 22.3 1.0
ND1 A:HIS563 4.1 24.1 1.0
CG A:HIS563 4.1 23.4 1.0
ND1 A:HIS529 4.2 26.1 1.0
CD2 A:HIS525 4.2 25.0 1.0
CG A:HIS529 4.2 26.1 1.0
CB A:ASP564 4.3 22.1 1.0
NE2 A:HIS525 4.4 24.6 1.0
CB A:ASP674 4.5 28.4 1.0
CG2 A:VAL533 4.7 23.3 1.0
O A:ASP674 4.8 28.9 1.0
O A:HOH928 4.8 21.2 1.0
CA A:ASP674 4.9 24.9 1.0

Zinc binding site 2 out of 4 in 5sf7

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One


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 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:27.6
occ:1.00
 NE2 B:HIS563 2.1 23.9 1.0
OD2 B:ASP564 2.1 24.0 1.0
OD1 B:ASP674 2.1 21.5 1.0
NE2 B:HIS529 2.2 22.3 1.0
O B:HOH942 2.2 21.6 1.0
O B:HOH966 2.3 22.6 1.0
CD2 B:HIS563 3.0 25.4 1.0
CG B:ASP674 3.1 22.7 1.0
CG B:ASP564 3.1 25.4 1.0
CE1 B:HIS563 3.1 26.6 1.0
CD2 B:HIS529 3.1 23.3 1.0
CE1 B:HIS529 3.3 26.5 1.0
OD2 B:ASP674 3.3 26.2 1.0
OD1 B:ASP564 3.6 23.9 1.0
MG B:MG802 3.8 25.2 1.0
O B:HOH975 4.0 20.1 1.0
O B:HOH932 4.1 24.8 1.0
CD2 B:HIS525 4.1 25.1 1.0
CG B:HIS563 4.2 24.6 1.0
ND1 B:HIS563 4.2 23.4 1.0
NE2 B:HIS525 4.2 25.1 1.0
CB B:ASP564 4.3 24.9 1.0
CG B:HIS529 4.3 25.3 1.0
ND1 B:HIS529 4.4 22.2 1.0
CB B:ASP674 4.4 23.1 1.0
O B:HOH941 4.6 19.5 1.0
CG2 B:VAL533 4.7 24.3 1.0
O B:ASP674 4.8 25.8 1.0
CA B:ASP674 4.8 24.6 1.0

Zinc binding site 3 out of 4 in 5sf7

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Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One


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 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:31.8
occ:1.00
 NE2 C:HIS563 2.1 27.5 1.0
O C:HOH1010 2.1 27.3 1.0
NE2 C:HIS529 2.1 26.8 1.0
O C:HOH931 2.2 23.6 1.0
OD1 C:ASP674 2.2 25.4 1.0
OD2 C:ASP564 2.2 27.2 1.0
CD2 C:HIS563 3.0 25.5 1.0
CD2 C:HIS529 3.1 27.2 1.0
CG C:ASP674 3.1 27.7 1.0
CG C:ASP564 3.1 27.4 1.0
CE1 C:HIS563 3.2 26.9 1.0
CE1 C:HIS529 3.2 29.8 1.0
OD2 C:ASP674 3.3 31.5 1.0
OD1 C:ASP564 3.6 27.2 1.0
MG C:MG802 3.9 26.2 1.0
O C:HOH915 4.1 28.9 1.0
CD2 C:HIS525 4.1 32.6 1.0
O C:HOH1024 4.2 23.8 1.0
CG C:HIS563 4.2 26.2 1.0
ND1 C:HIS563 4.2 24.8 1.0
CG C:HIS529 4.2 28.9 1.0
ND1 C:HIS529 4.3 26.3 1.0
CB C:ASP564 4.3 24.2 1.0
NE2 C:HIS525 4.3 32.7 1.0
CB C:ASP674 4.4 32.2 1.0
O C:HOH944 4.6 29.1 1.0
CG2 C:VAL533 4.8 26.3 1.0
CA C:ASP674 4.8 29.5 1.0
O C:ASP674 4.9 31.6 1.0

Zinc binding site 4 out of 4 in 5sf7

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Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One


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 1-(2- Chlorophenyl)-8-Methoxy-3,4-Dimethylimidazo[1,5-A]Quinazolin-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:35.7
occ:1.00
 NE2 D:HIS563 2.2 25.4 1.0
NE2 D:HIS529 2.2 38.4 1.0
O D:HOH933 2.2 27.5 1.0
OD2 D:ASP564 2.2 33.4 1.0
OD1 D:ASP674 2.3 29.8 1.0
O D:HOH958 2.3 28.5 1.0
CD2 D:HIS563 3.0 27.5 1.0
CD2 D:HIS529 3.1 38.3 1.0
CG D:ASP564 3.1 29.7 1.0
CG D:ASP674 3.2 33.2 1.0
CE1 D:HIS529 3.2 37.9 1.0
CE1 D:HIS563 3.3 29.4 1.0
OD2 D:ASP674 3.4 38.3 1.0
OD1 D:ASP564 3.7 29.8 1.0
MG D:MG802 3.9 31.5 1.0
CD2 D:HIS525 4.1 34.7 1.0
O D:HOH925 4.1 35.8 1.0
O D:HOH986 4.1 31.6 1.0
CG D:HIS563 4.2 27.7 1.0
CB D:ASP564 4.2 29.7 1.0
CG D:HIS529 4.3 35.7 1.0
ND1 D:HIS529 4.3 36.0 1.0
ND1 D:HIS563 4.3 26.7 1.0
NE2 D:HIS525 4.4 40.0 1.0
CB D:ASP674 4.6 30.3 1.0
O D:HOH926 4.6 29.7 1.0
CG2 D:VAL533 4.7 34.9 1.0
O D:ASP674 4.8 34.0 1.0
CA D:ASP674 4.9 30.7 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 04:51:34 2024

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