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Zinc in PDB 5edi: Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5%

Enzymatic activity of Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5%

All present enzymatic activity of Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5%:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5%, PDB code: 5edi 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) 43.60 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.231, 135.231, 235.395, 90.00, 90.00, 120.00
R / Rfree (%) 18.6 / 23.5

Other elements in 5edi:

The structure of Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5% also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5% (pdb code 5edi). 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, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5%, PDB code: 5edi:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5edi

Go back to Zinc Binding Sites List in 5edi
Zinc binding site 1 out of 4 in the Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5%


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:40.5
occ:1.00
 NE2 A:HIS563 2.1 33.1 1.0
O A:HOH953 2.1 34.9 1.0
OD2 A:ASP564 2.2 39.1 1.0
OD1 A:ASP674 2.2 39.4 1.0
NE2 A:HIS529 2.2 40.6 1.0
O A:HOH960 2.4 46.5 1.0
CD2 A:HIS563 3.0 34.1 1.0
CG A:ASP674 3.0 38.4 1.0
CG A:ASP564 3.1 37.0 1.0
CD2 A:HIS529 3.1 37.0 1.0
CE1 A:HIS563 3.1 33.9 1.0
OD2 A:ASP674 3.2 36.9 1.0
CE1 A:HIS529 3.2 37.3 1.0
OD1 A:ASP564 3.5 35.7 1.0
MG A:MG802 3.7 35.6 1.0
CD2 A:HIS525 4.1 39.9 1.0
CG A:HIS563 4.1 32.9 1.0
ND1 A:HIS563 4.2 31.0 1.0
O A:HOH973 4.3 31.9 1.0
O A:HOH942 4.3 49.8 1.0
CG A:HIS529 4.3 40.2 1.0
ND1 A:HIS529 4.3 38.6 1.0
CB A:ASP564 4.4 32.2 1.0
CB A:ASP674 4.5 36.0 1.0
NE2 A:HIS525 4.5 37.1 1.0
O A:HOH911 4.5 27.4 1.0
CG2 A:VAL533 4.7 31.2 1.0
O A:ASP674 4.9 38.6 1.0
CA A:ASP674 4.9 37.7 1.0

Zinc binding site 2 out of 4 in 5edi

Go back to Zinc Binding Sites List in 5edi
Zinc binding site 2 out of 4 in the Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5%


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5% within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:39.6
occ:1.00
 O B:HOH960 2.0 24.8 1.0
NE2 B:HIS563 2.1 32.8 1.0
NE2 B:HIS529 2.1 29.7 1.0
OD1 B:ASP674 2.2 36.0 1.0
OD2 B:ASP564 2.2 33.3 1.0
O B:HOH977 2.4 47.2 1.0
CD2 B:HIS529 3.0 34.4 1.0
CD2 B:HIS563 3.0 34.8 1.0
CG B:ASP674 3.1 35.7 1.0
CE1 B:HIS563 3.1 32.5 1.0
CE1 B:HIS529 3.2 33.4 1.0
CG B:ASP564 3.2 30.9 1.0
OD2 B:ASP674 3.3 33.3 1.0
OD1 B:ASP564 3.6 30.6 1.0
MG B:MG802 3.8 29.6 1.0
CD2 B:HIS525 4.0 41.4 1.0
O B:HOH979 4.1 31.0 1.0
ND1 B:HIS563 4.2 31.9 1.0
CG B:HIS563 4.2 33.4 1.0
O B:HOH949 4.2 37.0 1.0
CG B:HIS529 4.2 32.8 1.0
ND1 B:HIS529 4.2 32.7 1.0
NE2 B:HIS525 4.4 43.5 1.0
CB B:ASP674 4.4 32.7 1.0
CB B:ASP564 4.5 31.2 1.0
O B:HOH922 4.6 34.3 1.0
CG2 B:VAL533 4.8 32.1 1.0
CA B:ASP674 4.9 31.6 1.0
O B:ASP674 4.9 34.1 1.0

Zinc binding site 3 out of 4 in 5edi

Go back to Zinc Binding Sites List in 5edi
Zinc binding site 3 out of 4 in the Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5%


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5% within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:40.7
occ:1.00
 O C:HOH925 2.0 28.9 1.0
OD2 C:ASP564 2.1 38.6 1.0
NE2 C:HIS529 2.2 34.9 1.0
OD1 C:ASP674 2.2 35.1 1.0
NE2 C:HIS563 2.2 32.5 1.0
O C:HOH938 2.5 52.0 1.0
CD2 C:HIS563 3.1 30.1 1.0
CG C:ASP564 3.1 36.9 1.0
CG C:ASP674 3.1 36.4 1.0
CD2 C:HIS529 3.1 32.8 1.0
CE1 C:HIS529 3.2 33.1 1.0
CE1 C:HIS563 3.3 32.4 1.0
OD2 C:ASP674 3.3 41.5 1.0
OD1 C:ASP564 3.6 35.7 1.0
MG C:MG802 3.8 32.9 1.0
CD2 C:HIS525 4.0 38.1 1.0
O C:HOH975 4.2 34.4 1.0
CG C:HIS563 4.3 31.4 1.0
ND1 C:HIS529 4.3 34.1 1.0
CG C:HIS529 4.3 31.7 1.0
CB C:ASP564 4.3 32.8 1.0
ND1 C:HIS563 4.3 31.4 1.0
NE2 C:HIS525 4.4 38.3 1.0
O C:HOH943 4.5 44.1 1.0
CB C:ASP674 4.5 36.8 1.0
O C:HOH937 4.5 37.2 1.0
O C:HOH1005 4.6 52.0 1.0
CG2 C:VAL533 4.8 35.2 1.0
CA C:ASP674 4.9 37.4 1.0
O C:ASP674 5.0 37.8 1.0

Zinc binding site 4 out of 4 in 5edi

Go back to Zinc Binding Sites List in 5edi
Zinc binding site 4 out of 4 in the Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5%


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human PDE10A, 6-Chloro-5,8-Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl- 2H-[1,2,4]Triazol-3-Yl)-Ethyl]-[1,2,4]Triazolo[1,5-A]Pyridine, 2.20A, H3, Rfree=23.5% within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:57.9
occ:1.00
 NE2 D:HIS563 2.1 46.9 1.0
O D:HOH927 2.1 39.3 1.0
OD2 D:ASP564 2.2 60.5 1.0
NE2 D:HIS529 2.2 50.1 1.0
O D:HOH915 2.3 49.0 1.0
OD1 D:ASP674 2.3 60.0 1.0
CD2 D:HIS563 2.9 46.2 1.0
CD2 D:HIS529 3.1 53.4 1.0
CG D:ASP674 3.1 55.1 1.0
CE1 D:HIS563 3.2 50.2 1.0
CG D:ASP564 3.2 50.6 1.0
CE1 D:HIS529 3.3 51.0 1.0
OD2 D:ASP674 3.4 56.5 1.0
OD1 D:ASP564 3.7 51.6 1.0
MG D:MG802 3.8 54.8 1.0
CD2 D:HIS525 4.1 56.6 1.0
CG D:HIS563 4.1 48.4 1.0
O D:HOH920 4.2 45.9 1.0
ND1 D:HIS563 4.2 51.2 1.0
CG D:HIS529 4.3 48.8 1.0
CB D:ASP564 4.3 49.5 1.0
ND1 D:HIS529 4.4 53.3 1.0
NE2 D:HIS525 4.5 59.1 1.0
CB D:ASP674 4.5 54.9 1.0
O D:HOH908 4.6 59.4 1.0
O D:HOH906 4.7 51.0 1.0
CG2 D:VAL533 4.7 44.1 1.0
O D:ASP674 4.9 60.6 1.0
CA D:ASP674 4.9 57.2 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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