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Zinc in PDB 5dh5: PDE10 Complexed with N-[(1-Methylpyrazol-4-Yl)Methyl]-5-[[(1S,2S)-2- (2-Pyridyl)Cyclopropyl]Methoxy]Pyrazolo[1,5-A]Pyrimidin-7-Amine

Enzymatic activity of PDE10 Complexed with N-[(1-Methylpyrazol-4-Yl)Methyl]-5-[[(1S,2S)-2- (2-Pyridyl)Cyclopropyl]Methoxy]Pyrazolo[1,5-A]Pyrimidin-7-Amine

All present enzymatic activity of PDE10 Complexed with N-[(1-Methylpyrazol-4-Yl)Methyl]-5-[[(1S,2S)-2- (2-Pyridyl)Cyclopropyl]Methoxy]Pyrazolo[1,5-A]Pyrimidin-7-Amine:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of PDE10 Complexed with N-[(1-Methylpyrazol-4-Yl)Methyl]-5-[[(1S,2S)-2- (2-Pyridyl)Cyclopropyl]Methoxy]Pyrazolo[1,5-A]Pyrimidin-7-Amine, PDB code: 5dh5 was solved by Y.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.13 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.510, 81.780, 158.960, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 23.3

Other elements in 5dh5:

The structure of PDE10 Complexed with N-[(1-Methylpyrazol-4-Yl)Methyl]-5-[[(1S,2S)-2- (2-Pyridyl)Cyclopropyl]Methoxy]Pyrazolo[1,5-A]Pyrimidin-7-Amine also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the PDE10 Complexed with N-[(1-Methylpyrazol-4-Yl)Methyl]-5-[[(1S,2S)-2- (2-Pyridyl)Cyclopropyl]Methoxy]Pyrazolo[1,5-A]Pyrimidin-7-Amine (pdb code 5dh5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the PDE10 Complexed with N-[(1-Methylpyrazol-4-Yl)Methyl]-5-[[(1S,2S)-2- (2-Pyridyl)Cyclopropyl]Methoxy]Pyrazolo[1,5-A]Pyrimidin-7-Amine, PDB code: 5dh5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5dh5

Go back to Zinc Binding Sites List in 5dh5
Zinc binding site 1 out of 2 in the PDE10 Complexed with N-[(1-Methylpyrazol-4-Yl)Methyl]-5-[[(1S,2S)-2- (2-Pyridyl)Cyclopropyl]Methoxy]Pyrazolo[1,5-A]Pyrimidin-7-Amine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of PDE10 Complexed with N-[(1-Methylpyrazol-4-Yl)Methyl]-5-[[(1S,2S)-2- (2-Pyridyl)Cyclopropyl]Methoxy]Pyrazolo[1,5-A]Pyrimidin-7-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:49.2
occ:1.00
 OD1 A:ASP664 2.0 32.5 1.0
OD2 A:ASP554 2.1 33.9 1.0
O A:HOH911 2.1 24.4 1.0
NE2 A:HIS519 2.3 31.0 1.0
NE2 A:HIS553 2.3 37.1 1.0
O A:HOH902 2.8 34.3 1.0
CG A:ASP664 2.9 37.0 1.0
CD2 A:HIS553 3.0 36.8 1.0
OD2 A:ASP664 3.1 39.1 1.0
CG A:ASP554 3.1 35.6 1.0
CD2 A:HIS519 3.2 32.4 1.0
CE1 A:HIS519 3.3 30.4 1.0
CE1 A:HIS553 3.5 37.4 1.0
OD1 A:ASP554 3.6 34.8 1.0
MG A:MG802 3.7 27.8 1.0
CD2 A:HIS515 3.8 33.7 1.0
O A:HOH966 4.0 31.4 1.0
NE2 A:HIS515 4.0 32.9 1.0
CG A:HIS553 4.2 35.8 1.0
CB A:ASP664 4.3 29.6 1.0
CB A:ASP554 4.4 32.1 1.0
CG A:HIS519 4.4 30.4 1.0
ND1 A:HIS553 4.4 37.6 1.0
ND1 A:HIS519 4.5 31.2 1.0
O A:HOH922 4.5 27.8 1.0
O A:HOH971 4.6 40.2 1.0
O A:HOH909 4.6 29.9 1.0
CA A:ASP664 4.8 26.7 1.0
CG2 A:VAL523 4.8 29.5 1.0
O A:ASP664 4.9 28.8 1.0
O A:HOH937 5.0 28.4 1.0

Zinc binding site 2 out of 2 in 5dh5

Go back to Zinc Binding Sites List in 5dh5
Zinc binding site 2 out of 2 in the PDE10 Complexed with N-[(1-Methylpyrazol-4-Yl)Methyl]-5-[[(1S,2S)-2- (2-Pyridyl)Cyclopropyl]Methoxy]Pyrazolo[1,5-A]Pyrimidin-7-Amine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of PDE10 Complexed with N-[(1-Methylpyrazol-4-Yl)Methyl]-5-[[(1S,2S)-2- (2-Pyridyl)Cyclopropyl]Methoxy]Pyrazolo[1,5-A]Pyrimidin-7-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:52.1
occ:1.00
 OD2 B:ASP554 2.1 33.8 1.0
OD1 B:ASP664 2.1 36.4 1.0
NE2 B:HIS519 2.1 28.9 1.0
NE2 B:HIS553 2.3 33.8 1.0
O B:HOH916 2.3 28.7 1.0
O B:HOH931 3.0 39.6 1.0
CG B:ASP664 3.0 37.5 1.0
CD2 B:HIS553 3.0 33.9 1.0
CD2 B:HIS519 3.0 29.4 1.0
CG B:ASP554 3.1 35.5 1.0
CE1 B:HIS519 3.2 28.5 1.0
OD2 B:ASP664 3.3 39.8 1.0
CE1 B:HIS553 3.4 33.2 1.0
OD1 B:ASP554 3.6 33.2 1.0
CD2 B:HIS515 3.8 36.5 1.0
MG B:MG802 3.9 29.7 1.0
NE2 B:HIS515 4.0 35.7 1.0
O B:HOH939 4.1 29.3 1.0
CG B:HIS553 4.2 32.5 1.0
CG B:HIS519 4.2 28.7 1.0
ND1 B:HIS519 4.3 29.8 1.0
CB B:ASP554 4.4 32.5 1.0
CB B:ASP664 4.4 26.9 1.0
ND1 B:HIS553 4.4 33.2 1.0
O B:HOH905 4.6 34.6 1.0
O B:HOH901 4.7 31.8 1.0
CG2 B:VAL523 4.7 29.0 1.0
CA B:ASP664 4.8 26.6 1.0
O B:HOH970 4.8 42.8 1.0
O B:ASP664 4.8 29.5 1.0

Reference:

I.T.Raheem, J.D.Schreier, J.Fuerst, L.Gantert, E.D.Hostetler, S.Huszar, A.Joshi, M.Kandebo, S.H.Kim, J.Li, B.Ma, G.Mcgaughey, S.Sharma, W.D.Shipe, J.Uslaner, G.H.Vandeveer, Y.Yan, J.J.Renger, S.M.Smith, P.J.Coleman, C.D.Cox. Discovery of Pyrazolopyrimidine Phosphodiesterase 10A Inhibitors For the Treatment of Schizophrenia. Bioorg.Med.Chem.Lett. V. 26 126 2016.
ISSN: ESSN 1464-3405
PubMed: 26602277
DOI: 10.1016/J.BMCL.2015.11.013
Page generated: Sun Oct 27 14:44:28 2024

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