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Zinc in PDB 5edh: Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7%

Enzymatic activity of Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7%

All present enzymatic activity of Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7%:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7%, PDB code: 5edh was solved by C.Joseph, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.68 / 2.03
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.401, 135.401, 235.335, 90.00, 90.00, 120.00
R / Rfree (%) 18.6 / 22.7

Other elements in 5edh:

The structure of Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7% also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7% (pdb code 5edh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7%, PDB code: 5edh:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5edh

Go back to Zinc Binding Sites List in 5edh
Zinc binding site 1 out of 4 in the Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7%


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:31.2
occ:1.00
 O A:HOH966 2.0 27.2 1.0
NE2 A:HIS529 2.1 28.5 1.0
NE2 A:HIS563 2.1 29.6 1.0
OD2 A:ASP564 2.2 30.4 1.0
OD1 A:ASP674 2.2 28.6 1.0
O A:HOH962 2.5 41.7 1.0
CD2 A:HIS563 3.0 26.6 1.0
CE1 A:HIS529 3.1 26.4 1.0
CG A:ASP564 3.1 29.1 1.0
CD2 A:HIS529 3.1 26.6 1.0
CG A:ASP674 3.2 27.6 1.0
CE1 A:HIS563 3.2 28.8 1.0
OD2 A:ASP674 3.4 30.9 1.0
OD1 A:ASP564 3.5 26.8 1.0
MG A:MG802 3.7 27.6 1.0
CD2 A:HIS525 4.0 28.1 1.0
CG A:HIS563 4.2 27.3 1.0
O A:HOH999 4.2 23.9 1.0
ND1 A:HIS529 4.2 27.0 1.0
ND1 A:HIS563 4.2 29.1 1.0
CG A:HIS529 4.3 28.3 1.0
CB A:ASP564 4.3 27.3 1.0
NE2 A:HIS525 4.4 29.6 1.0
O A:HOH970 4.5 35.7 1.0
CB A:ASP674 4.5 27.4 1.0
O A:HOH908 4.5 24.4 1.0
CG2 A:VAL533 4.7 24.3 1.0
CA A:ASP674 4.8 25.6 1.0
O A:ASP674 4.9 28.1 1.0

Zinc binding site 2 out of 4 in 5edh

Go back to Zinc Binding Sites List in 5edh
Zinc binding site 2 out of 4 in the Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7%


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:28.9
occ:1.00
 OD1 B:ASP674 2.2 27.0 1.0
O B:HOH975 2.2 24.3 1.0
NE2 B:HIS563 2.2 25.5 1.0
OD2 B:ASP564 2.2 25.2 1.0
NE2 B:HIS529 2.2 22.7 1.0
O B:HOH915 2.9 50.9 1.0
CG B:ASP674 3.0 28.2 1.0
CD2 B:HIS563 3.0 25.1 1.0
CD2 B:HIS529 3.1 26.5 1.0
CG B:ASP564 3.2 25.1 1.0
CE1 B:HIS563 3.2 24.9 1.0
OD2 B:ASP674 3.2 29.5 1.0
CE1 B:HIS529 3.3 26.0 1.0
OD1 B:ASP564 3.6 25.4 1.0
MG B:MG802 3.8 25.1 1.0
CD2 B:HIS525 3.9 24.1 1.0
O B:HOH1004 4.1 23.1 1.0
CG B:HIS563 4.2 25.5 1.0
ND1 B:HIS563 4.3 25.4 1.0
CG B:HIS529 4.3 25.3 1.0
NE2 B:HIS525 4.3 26.8 1.0
ND1 B:HIS529 4.4 24.0 1.0
CB B:ASP564 4.4 23.2 1.0
CB B:ASP674 4.4 27.4 1.0
O B:HOH972 4.5 37.0 1.0
O B:HOH951 4.5 24.9 1.0
CG2 B:VAL533 4.7 18.8 1.0
O B:HOH1042 4.7 47.2 1.0
CA B:ASP674 4.9 25.3 1.0
O B:ASP674 5.0 24.3 1.0
O B:HOH927 5.0 20.3 1.0

Zinc binding site 3 out of 4 in 5edh

Go back to Zinc Binding Sites List in 5edh
Zinc binding site 3 out of 4 in the Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7%


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:31.0
occ:1.00
 O C:HOH954 2.1 24.6 1.0
NE2 C:HIS529 2.2 27.4 1.0
NE2 C:HIS563 2.2 25.1 1.0
OD2 C:ASP564 2.2 24.8 1.0
OD1 C:ASP674 2.2 24.9 1.0
O C:HOH941 2.5 49.2 1.0
CD2 C:HIS563 3.0 24.2 1.0
CD2 C:HIS529 3.1 28.9 1.0
CG C:ASP674 3.1 27.5 1.0
CG C:ASP564 3.1 24.8 1.0
CE1 C:HIS529 3.2 29.1 1.0
CE1 C:HIS563 3.3 24.8 1.0
OD2 C:ASP674 3.3 31.7 1.0
OD1 C:ASP564 3.6 25.8 1.0
MG C:MG802 3.8 26.1 1.0
CD2 C:HIS525 3.9 28.4 1.0
O C:HOH1001 4.2 23.4 1.0
CG C:HIS563 4.2 25.0 1.0
CG C:HIS529 4.2 28.5 1.0
ND1 C:HIS529 4.3 26.8 1.0
ND1 C:HIS563 4.3 24.6 1.0
NE2 C:HIS525 4.3 29.4 1.0
CB C:ASP564 4.3 23.9 1.0
CB C:ASP674 4.5 26.1 1.0
O C:HOH943 4.5 25.1 1.0
O C:HOH986 4.5 38.2 1.0
O C:HOH1033 4.6 48.9 1.0
CG2 C:VAL533 4.7 22.9 1.0
CA C:ASP674 4.9 27.9 1.0
O C:ASP674 5.0 29.1 1.0

Zinc binding site 4 out of 4 in 5edh

Go back to Zinc Binding Sites List in 5edh
Zinc binding site 4 out of 4 in the Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7%


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human PDE10A, 8-Ethyl-5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4- Triazol-3-Yl)Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, 2.03A, H3, Rfree=22.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:39.8
occ:1.00
 O D:HOH923 1.9 30.2 1.0
NE2 D:HIS563 2.2 33.8 1.0
NE2 D:HIS529 2.3 40.3 1.0
OD2 D:ASP564 2.3 36.0 1.0
OD1 D:ASP674 2.3 33.8 1.0
O D:HOH914 2.6 53.8 1.0
CD2 D:HIS563 2.9 33.6 1.0
CG D:ASP674 3.1 32.9 1.0
CG D:ASP564 3.2 34.2 1.0
CD2 D:HIS529 3.2 41.7 1.0
CE1 D:HIS529 3.2 38.7 1.0
OD2 D:ASP674 3.3 35.8 1.0
CE1 D:HIS563 3.4 36.3 1.0
OD1 D:ASP564 3.6 34.0 1.0
MG D:MG802 3.8 40.4 1.0
CD2 D:HIS525 4.0 37.3 1.0
O D:HOH935 4.1 36.4 1.0
CG D:HIS563 4.2 32.8 1.0
ND1 D:HIS529 4.4 39.7 1.0
ND1 D:HIS563 4.4 35.1 1.0
CB D:ASP564 4.4 34.7 1.0
CG D:HIS529 4.4 39.1 1.0
NE2 D:HIS525 4.4 43.1 1.0
O D:HOH954 4.5 47.0 1.0
CB D:ASP674 4.5 32.5 1.0
O D:HOH903 4.5 34.1 1.0
CG2 D:VAL533 4.7 34.4 1.0
O D:ASP674 4.9 36.4 1.0
CA D:ASP674 4.9 34.0 1.0

Reference:

B.Kuhn, W.Guba, J.Hert, D.Banner, C.Bissantz, S.Ceccarelli, W.Haap, M.Korner, A.Kuglstatter, C.Lerner, P.Mattei, W.Neidhart, E.Pinard, M.G.Rudolph, T.Schulz-Gasch, T.Woltering, M.Stahl. A Real-World Perspective on Molecular Design. J.Med.Chem. V. 59 4087 2016.
ISSN: ISSN 0022-2623
PubMed: 26878596
DOI: 10.1021/ACS.JMEDCHEM.5B01875
Page generated: Sun Oct 27 15:11:09 2024

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