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Chlorine 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
Zinc (Zn) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5edi

Go back to Chlorine Binding Sites List in 5edi
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl803

b:49.3
occ:1.00
 CL1 A:5M9803 0.0 49.3 1.0
C01 A:5M9803 1.7 39.0 1.0
C02 A:5M9803 2.7 40.9 1.0
C04 A:5M9803 2.8 42.1 1.0
C23 A:5M9803 3.2 41.1 1.0
O A:HOH952 3.5 41.3 1.0
O A:LEU675 3.5 38.2 1.0
CG1 A:VAL678 3.7 40.1 1.0
CA A:LEU675 3.8 38.6 1.0
OG A:SER677 3.9 51.5 1.0
C A:LEU675 3.9 36.1 1.0
CB A:SER677 4.0 43.3 1.0
C03 A:5M9803 4.0 41.3 1.0
N05 A:5M9803 4.1 42.1 1.0
CD2 A:LEU675 4.2 42.0 1.0
CD1 A:ILE692 4.2 40.0 1.0
OH A:TYR524 4.2 48.6 1.0
CB A:LEU675 4.2 40.3 1.0
O A:HOH942 4.3 49.8 1.0
N A:VAL678 4.5 38.4 1.0
C06 A:5M9803 4.6 39.9 1.0
CE2 A:PHE729 4.6 37.8 1.0
O A:ASP674 4.6 38.6 1.0
N A:SER677 4.7 36.9 1.0
CA A:SER677 4.8 39.9 1.0
CG A:LEU675 4.8 42.1 1.0
O A:HOH906 4.9 33.0 1.0
CB A:VAL678 5.0 42.0 1.0
N A:CYS676 5.0 36.4 1.0
CZ A:PHE729 5.0 39.0 1.0

Chlorine binding site 2 out of 4 in 5edi

Go back to Chlorine Binding Sites List in 5edi
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl803

b:49.9
occ:1.00
 CL1 B:5M9803 0.0 49.9 1.0
C01 B:5M9803 1.7 41.8 1.0
C02 B:5M9803 2.7 42.4 1.0
C04 B:5M9803 2.8 41.3 1.0
O B:HOH938 3.1 49.4 1.0
C23 B:5M9803 3.2 37.6 1.0
O B:LEU675 3.4 38.1 1.0
CB B:SER677 3.7 44.3 1.0
CA B:LEU675 3.7 36.4 1.0
CG1 B:VAL678 3.8 40.7 1.0
C B:LEU675 3.9 37.2 1.0
OH B:TYR524 3.9 43.7 1.0
CD2 B:LEU675 4.0 38.8 1.0
C03 B:5M9803 4.0 42.0 1.0
OG B:SER677 4.1 55.7 1.0
N05 B:5M9803 4.1 42.0 1.0
CD1 B:ILE692 4.1 40.4 1.0
CB B:LEU675 4.2 37.7 1.0
O B:HOH949 4.4 37.0 1.0
N B:SER677 4.5 42.7 1.0
N B:VAL678 4.5 45.0 1.0
CE2 B:PHE729 4.6 36.7 1.0
CA B:SER677 4.6 45.1 1.0
O B:ASP674 4.6 34.1 1.0
C06 B:5M9803 4.6 41.5 1.0
CG B:LEU675 4.7 39.6 1.0
C B:SER677 4.9 47.2 1.0
CZ B:TYR524 4.9 42.2 1.0
N B:CYS676 5.0 38.7 1.0
N B:LEU675 5.0 36.3 1.0

Chlorine binding site 3 out of 4 in 5edi

Go back to Chlorine Binding Sites List in 5edi
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl803

b:47.7
occ:1.00
 CL1 C:5M9803 0.0 47.7 1.0
C01 C:5M9803 1.7 42.2 1.0
C02 C:5M9803 2.7 42.3 1.0
C04 C:5M9803 2.8 42.0 1.0
OG C:SER677 3.1 52.7 1.0
C23 C:5M9803 3.2 41.5 1.0
O C:HOH930 3.4 48.5 1.0
O C:LEU675 3.6 38.3 1.0
CG1 C:VAL678 3.8 41.6 1.0
OH C:TYR524 3.9 46.4 1.0
CA C:LEU675 4.0 35.4 1.0
CD1 C:ILE692 4.0 46.9 1.0
C C:LEU675 4.0 34.5 1.0
C03 C:5M9803 4.0 45.3 1.0
N05 C:5M9803 4.1 44.8 1.0
O C:HOH943 4.1 44.1 1.0
CD2 C:LEU675 4.2 34.4 1.0
CB C:SER677 4.3 47.1 1.0
CB C:LEU675 4.5 36.8 1.0
N C:VAL678 4.5 41.8 1.0
C06 C:5M9803 4.6 44.7 1.0
O C:ASP674 4.6 37.8 1.0
CE2 C:PHE729 4.6 45.1 1.0
N C:SER677 4.6 40.8 1.0
CA C:SER677 4.8 47.4 1.0
CZ C:TYR524 4.9 45.3 1.0
O C:HOH987 4.9 46.6 1.0
CZ C:PHE729 4.9 41.6 1.0
C C:SER677 5.0 46.1 1.0

Chlorine binding site 4 out of 4 in 5edi

Go back to Chlorine Binding Sites List in 5edi
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl803

b:70.1
occ:1.00
 CL1 D:5M9803 0.0 70.1 1.0
C01 D:5M9803 1.7 58.7 1.0
C04 D:5M9803 2.7 57.7 1.0
C02 D:5M9803 2.7 58.5 1.0
C23 D:5M9803 3.1 53.3 1.0
OG D:SER677 3.2 76.3 1.0
O D:LEU675 3.4 57.0 1.0
CG1 D:VAL678 3.8 60.1 1.0
C D:LEU675 3.9 57.4 1.0
CA D:LEU675 3.9 59.8 1.0
CD1 D:ILE692 4.0 63.0 1.0
OH D:TYR524 4.0 78.1 1.0
C03 D:5M9803 4.1 58.0 1.0
N05 D:5M9803 4.1 60.1 1.0
CB D:SER677 4.3 66.8 1.0
O D:HOH908 4.3 59.4 1.0
N D:VAL678 4.4 57.9 1.0
CB D:LEU675 4.5 59.5 1.0
N D:SER677 4.6 62.3 1.0
CD2 D:LEU675 4.6 61.2 1.0
C06 D:5M9803 4.6 56.2 1.0
CE2 D:PHE729 4.6 57.1 1.0
CA D:SER677 4.8 65.2 1.0
O D:ASP674 4.8 60.6 1.0
CB D:VAL678 4.9 58.6 1.0
C D:SER677 4.9 62.5 1.0
O D:HOH902 5.0 58.5 1.0
N D:CYS676 5.0 55.9 1.0
CZ D:TYR524 5.0 73.5 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: Fri Jul 26 07:15:36 2024

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