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Zinc in PDB 5sed: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine, PDB code: 5sed was solved by C.Joseph, K.Groebke-Zbinden, 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) 43.49 / 2.32
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.193, 135.193, 235.868, 90, 90, 120
R / Rfree (%) 19.2 / 24.2

Other elements in 5sed:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine 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 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine (pdb code 5sed). 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-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine, PDB code: 5sed:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sed

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine


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-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:31.2
occ:1.00
 OD2 A:ASP564 1.9 25.3 1.0
NE2 A:HIS529 2.1 35.8 1.0
NE2 A:HIS563 2.1 25.0 1.0
O A:HOH934 2.2 20.7 1.0
OD1 A:ASP674 2.2 30.8 1.0
O A:HOH946 2.6 36.3 1.0
CD2 A:HIS563 3.0 25.8 1.0
CG A:ASP564 3.0 25.4 1.0
CE1 A:HIS529 3.1 32.1 1.0
CG A:ASP674 3.1 31.8 1.0
CD2 A:HIS529 3.1 32.0 1.0
CE1 A:HIS563 3.2 26.9 1.0
OD2 A:ASP674 3.3 40.9 1.0
OD1 A:ASP564 3.6 23.4 1.0
MG A:MG802 3.8 24.6 1.0
O A:HOH965 4.1 20.6 1.0
CG A:HIS563 4.2 25.6 1.0
ND1 A:HIS529 4.2 32.4 1.0
CB A:ASP564 4.2 25.9 1.0
CD2 A:HIS525 4.2 29.7 1.0
ND1 A:HIS563 4.2 24.4 1.0
CG A:HIS529 4.2 29.6 1.0
O A:HOH942 4.4 32.1 1.0
CB A:ASP674 4.5 34.0 1.0
NE2 A:HIS525 4.5 28.4 1.0
O A:HOH929 4.6 20.4 1.0
CG2 A:VAL533 4.7 22.8 1.0
O A:ASP674 4.7 31.4 1.0
O A:HOH991 4.7 45.1 1.0
CA A:ASP674 4.9 28.9 1.0

Zinc binding site 2 out of 4 in 5sed

Go back to Zinc Binding Sites List in 5sed
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine


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-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:31.1
occ:1.00
 NE2 B:HIS563 2.0 25.9 1.0
O B:HOH929 2.0 16.2 1.0
OD2 B:ASP564 2.0 23.9 1.0
OD1 B:ASP674 2.2 29.6 1.0
NE2 B:HIS529 2.2 27.1 1.0
O B:HOH956 2.4 29.8 1.0
CD2 B:HIS563 3.0 27.3 1.0
CE1 B:HIS563 3.0 26.1 1.0
CG B:ASP674 3.0 28.6 1.0
CG B:ASP564 3.0 23.6 1.0
CD2 B:HIS529 3.2 27.2 1.0
OD2 B:ASP674 3.2 28.7 1.0
CE1 B:HIS529 3.3 26.8 1.0
OD1 B:ASP564 3.5 22.1 1.0
MG B:MG802 3.9 21.4 1.0
ND1 B:HIS563 4.1 27.2 1.0
O B:HOH982 4.1 18.9 1.0
CG B:HIS563 4.1 25.4 1.0
O B:HOH967 4.1 32.2 1.0
CD2 B:HIS525 4.2 27.2 1.0
CB B:ASP564 4.3 22.6 1.0
CG B:HIS529 4.3 25.6 1.0
ND1 B:HIS529 4.4 26.9 1.0
CB B:ASP674 4.4 29.2 1.0
NE2 B:HIS525 4.4 28.9 1.0
O B:HOH914 4.5 22.2 1.0
CG2 B:VAL533 4.8 25.0 1.0
O B:ASP674 4.8 30.4 1.0
CA B:ASP674 4.9 26.1 1.0

Zinc binding site 3 out of 4 in 5sed

Go back to Zinc Binding Sites List in 5sed
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine


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-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:33.4
occ:1.00
 NE2 C:HIS563 2.0 31.1 1.0
O C:HOH930 2.1 20.2 1.0
OD2 C:ASP564 2.1 25.9 1.0
NE2 C:HIS529 2.1 27.1 1.0
OD1 C:ASP674 2.2 28.4 1.0
O C:HOH975 2.3 31.5 1.0
CD2 C:HIS563 2.9 29.0 1.0
CD2 C:HIS529 3.1 25.2 1.0
CE1 C:HIS563 3.1 30.3 1.0
CG C:ASP674 3.1 26.7 1.0
CG C:ASP564 3.1 27.0 1.0
CE1 C:HIS529 3.2 28.2 1.0
OD2 C:ASP674 3.4 27.9 1.0
OD1 C:ASP564 3.6 30.2 1.0
MG C:MG802 3.8 23.4 1.0
CG C:HIS563 4.1 27.1 1.0
CD2 C:HIS525 4.1 34.1 1.0
ND1 C:HIS563 4.2 26.4 1.0
CG C:HIS529 4.3 26.4 1.0
ND1 C:HIS529 4.3 27.1 1.0
CB C:ASP564 4.3 25.6 1.0
O C:HOH939 4.4 25.6 1.0
O C:HOH912 4.4 22.4 1.0
NE2 C:HIS525 4.4 30.5 1.0
O C:HOH988 4.5 26.7 1.0
CB C:ASP674 4.5 28.4 1.0
CG2 C:VAL533 4.8 26.1 1.0
CA C:ASP674 4.8 28.1 1.0
O C:ASP674 4.9 31.6 1.0

Zinc binding site 4 out of 4 in 5sed

Go back to Zinc Binding Sites List in 5sed
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine


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-[6- Chloro-2-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinazolin-4- Yl]Morpholine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:44.5
occ:1.00
 OD2 D:ASP564 2.0 55.3 1.0
NE2 D:HIS563 2.1 34.2 1.0
NE2 D:HIS529 2.2 44.5 1.0
O D:HOH909 2.2 26.9 1.0
OD1 D:ASP674 2.2 40.0 1.0
O D:HOH912 2.4 40.8 1.0
CD2 D:HIS563 2.9 34.4 1.0
CG D:ASP564 3.1 46.1 1.0
CD2 D:HIS529 3.1 43.6 1.0
CG D:ASP674 3.1 37.8 1.0
CE1 D:HIS563 3.2 36.3 1.0
CE1 D:HIS529 3.2 42.5 1.0
OD2 D:ASP674 3.3 40.5 1.0
OD1 D:ASP564 3.7 45.4 1.0
MG D:MG802 3.9 38.8 1.0
O D:HOH928 4.1 39.3 1.0
CD2 D:HIS525 4.1 46.1 1.0
CG D:HIS563 4.1 35.7 1.0
O D:HOH922 4.2 33.0 1.0
CB D:ASP564 4.2 41.5 1.0
ND1 D:HIS563 4.2 35.1 1.0
CG D:HIS529 4.3 43.5 1.0
ND1 D:HIS529 4.3 43.7 1.0
NE2 D:HIS525 4.5 44.4 1.0
CB D:ASP674 4.5 40.7 1.0
O D:HOH902 4.6 32.4 1.0
CG2 D:VAL533 4.7 45.2 1.0
O D:ASP674 4.8 45.8 1.0
CA D:ASP674 4.9 42.0 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 04:38:43 2024

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