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Magnesium in PDB 5xkm: Crystal Structure of Human Phosphodiesterase 2A in Complex with 6- Methyl-N-(1-(4-(Trifluoromethoxy)Phenyl)Propyl)Pyrazolo[1,5- A]Pyrimidine-3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 2A in Complex with 6- Methyl-N-(1-(4-(Trifluoromethoxy)Phenyl)Propyl)Pyrazolo[1,5- A]Pyrimidine-3-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 2A in Complex with 6- Methyl-N-(1-(4-(Trifluoromethoxy)Phenyl)Propyl)Pyrazolo[1,5- A]Pyrimidine-3-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 2A in Complex with 6- Methyl-N-(1-(4-(Trifluoromethoxy)Phenyl)Propyl)Pyrazolo[1,5- A]Pyrimidine-3-Carboxamide, PDB code: 5xkm was solved by H.Oki, M.Kondo, G.Snell, W.Lane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 84.82 / 2.16
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 72.925, 89.768, 90.361, 107.31, 113.85, 89.84
R / Rfree (%) 20.2 / 25.6

Other elements in 5xkm:

The structure of Crystal Structure of Human Phosphodiesterase 2A in Complex with 6- Methyl-N-(1-(4-(Trifluoromethoxy)Phenyl)Propyl)Pyrazolo[1,5- A]Pyrimidine-3-Carboxamide also contains other interesting chemical elements:

Fluorine (F) 18 atoms
Zinc (Zn) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 6- Methyl-N-(1-(4-(Trifluoromethoxy)Phenyl)Propyl)Pyrazolo[1,5- A]Pyrimidine-3-Carboxamide (pdb code 5xkm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 6- Methyl-N-(1-(4-(Trifluoromethoxy)Phenyl)Propyl)Pyrazolo[1,5- A]Pyrimidine-3-Carboxamide, PDB code: 5xkm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5xkm

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Magnesium binding site 1 out of 8 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 6- Methyl-N-(1-(4-(Trifluoromethoxy)Phenyl)Propyl)Pyrazolo[1,5- A]Pyrimidine-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Phosphodiesterase 2A in Complex with 6- Methyl-N-(1-(4-(Trifluoromethoxy)Phenyl)Propyl)Pyrazolo[1,5- A]Pyrimidine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2001

b:15.5
occ:1.00
 OD1 A:ASP697 2.0 10.3 1.0
O A:HOH2167 2.1 7.3 1.0
O A:HOH2116 2.1 10.3 1.0
O A:HOH2105 2.2 13.7 1.0
O A:HOH2124 2.2 13.0 1.0
O A:HOH2143 2.2 11.2 1.0
CG A:ASP697 3.0 10.2 1.0
OD2 A:ASP697 3.4 10.0 1.0
ZN A:ZN2002 3.8 15.2 1.0
NE2 A:HIS730 3.9 11.4 1.0
O A:HOH2145 4.0 16.3 1.0
O A:HOH2161 4.1 12.9 1.0
OE2 A:GLU727 4.2 12.1 1.0
CD2 A:HIS696 4.2 11.0 1.0
CD2 A:HIS700 4.2 18.5 1.0
O A:HIS696 4.2 11.6 1.0
CD2 A:HIS730 4.2 11.2 1.0
OG1 A:THR768 4.3 13.2 1.0
CB A:ASP697 4.3 10.2 1.0
NE2 A:HIS700 4.5 19.1 1.0
NE2 A:HIS696 4.5 11.3 1.0
OD2 A:ASP808 4.5 9.9 1.0
CB A:THR768 4.6 13.1 1.0
NE2 A:HIS656 4.6 14.4 1.0
CD2 A:HIS656 4.7 14.2 1.0
CA A:ASP697 4.7 10.6 1.0
O A:THR768 4.8 12.2 1.0
C A:HIS696 5.0 11.1 1.0

Magnesium binding site 2 out of 8 in 5xkm

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Magnesium binding site 2 out of 8 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 6- Methyl-N-(1-(4-(Trifluoromethoxy)Phenyl)Propyl)Pyrazolo[1,5- A]Pyrimidine-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Phosphodiesterase 2A in Complex with 6- Methyl-N-(1-(4-(Trifluoromethoxy)Phenyl)Propyl)Pyrazolo[1,5- A]Pyrimidine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2003

b:35.0
occ:1.00
 O A:HOH2196 1.9 27.6 1.0
O A:HOH2213 2.0 33.1 1.0
O A:HOH2190 2.1 17.9 1.0
O A:HOH2154 2.1 20.2 1.0
O A:GLU785 2.1 24.5 1.0
OE2 A:GLU785 2.7 36.5 1.0
C A:GLU785 3.2 25.2 1.0
CD A:GLU785 3.4 40.4 1.0
OE1 A:GLU785 3.7 51.6 1.0
CA A:GLU785 3.8 26.4 1.0
O A:HOH2175 4.1 27.9 1.0
O A:ALA784 4.4 20.9 1.0
O A:HOH2229 4.4 21.7 1.0
N A:VAL786 4.4 23.0 1.0
CG A:GLU785 4.5 35.6 1.0
CB A:GLU785 4.6 28.5 1.0
O A:HOH2237 4.6 34.7 1.0
CA A:VAL786 4.8 22.4 1.0
C A:VAL786 4.9 23.1 1.0
N A:GLU785 4.9 25.1 1.0
N A:GLY787 5.0 21.0 1.0

Magnesium binding site 3 out of 8 in 5xkm

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Magnesium binding site 3 out of 8 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 6- Methyl-N-(1-(4-(Trifluoromethoxy)Phenyl)Propyl)Pyrazolo[1,5- A]Pyrimidine-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Phosphodiesterase 2A in Complex with 6- Methyl-N-(1-(4-(Trifluoromethoxy)Phenyl)Propyl)Pyrazolo[1,5- A]Pyrimidine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:17.0
occ:1.00
 O B:HOH2154 2.0 6.9 1.0
O B:HOH2144 2.0 13.2 1.0
O B:HOH2110 2.2 13.4 1.0
OD1 B:ASP697 2.2 11.9 1.0
O B:HOH2106 2.2 8.6 1.0
O B:HOH2142 2.3 10.3 1.0
CG B:ASP697 3.2 12.4 1.0
OD2 B:ASP697 3.5 11.5 1.0
ZN B:ZN2002 3.9 17.5 1.0
OE2 B:GLU727 3.9 14.8 1.0
O B:HOH2172 4.0 17.1 1.0
O B:HOH2132 4.1 12.0 1.0
NE2 B:HIS730 4.1 11.7 1.0
OG1 B:THR768 4.2 15.8 1.0
CD2 B:HIS696 4.3 10.0 1.0
O B:HIS696 4.3 10.5 1.0
NE2 B:HIS656 4.3 15.6 1.0
CD2 B:HIS730 4.4 11.5 1.0
CD2 B:HIS700 4.5 14.8 1.0
OD2 B:ASP808 4.5 13.4 1.0
CB B:ASP697 4.6 11.9 1.0
CD2 B:HIS656 4.6 15.3 1.0
CB B:THR768 4.6 15.8 1.0
NE2 B:HIS696 4.7 9.8 1.0
O B:THR768 4.7 17.3 1.0
NE2 B:HIS700 4.8 14.7 1.0
CA B:ASP697 4.9 11.9 1.0
CD B:GLU727 4.9 16.6 1.0

Magnesium binding site 4 out of 8 in 5xkm

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Magnesium binding site 4 out of 8 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 6- Methyl-N-(1-(4-(Trifluoromethoxy)Phenyl)Propyl)Pyrazolo[1,5- A]Pyrimidine-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human Phosphodiesterase 2A in Complex with 6- Methyl-N-(1-(4-(Trifluoromethoxy)Phenyl)Propyl)Pyrazolo[1,5- A]Pyrimidine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2001

b:15.2
occ:1.00
 O C:HOH2136 2.0 10.1 1.0
O C:HOH2114 2.0 13.7 1.0
O C:HOH2137 2.1 9.2 1.0
OD1 C:ASP697 2.1 12.2 1.0
O C:HOH2103 2.2 10.9 1.0
O C:HOH2149 2.2 8.5 1.0
CG C:ASP697 3.1 12.8 1.0
OD2 C:ASP697 3.4 11.5 1.0
ZN C:ZN2002 3.8 17.7 1.0
O C:HOH2119 3.9 18.2 1.0
OE2 C:GLU727 4.0 18.2 1.0
O C:HOH2121 4.0 20.3 1.0
NE2 C:HIS730 4.2 9.7 1.0
CD2 C:HIS696 4.2 11.7 1.0
OG1 C:THR768 4.3 15.8 1.0
O C:HIS696 4.3 13.4 1.0
NE2 C:HIS656 4.4 15.5 1.0
CD2 C:HIS730 4.4 10.5 1.0
CB C:ASP697 4.5 12.4 1.0
OD2 C:ASP808 4.5 12.2 1.0
CD2 C:HIS700 4.5 15.6 1.0
CB C:THR768 4.6 14.7 1.0
CD2 C:HIS656 4.6 15.2 1.0
NE2 C:HIS696 4.7 11.7 1.0
O C:THR768 4.7 14.3 1.0
NE2 C:HIS700 4.8 16.2 1.0
CA C:ASP697 4.9 13.0 1.0
CD C:GLU727 4.9 18.7 1.0
CG C:GLU727 5.0 17.8 1.0

Magnesium binding site 5 out of 8 in 5xkm

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Magnesium binding site 5 out of 8 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 6- Methyl-N-(1-(4-(Trifluoromethoxy)Phenyl)Propyl)Pyrazolo[1,5- A]Pyrimidine-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Human Phosphodiesterase 2A in Complex with 6- Methyl-N-(1-(4-(Trifluoromethoxy)Phenyl)Propyl)Pyrazolo[1,5- A]Pyrimidine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2001

b:14.6
occ:1.00
 O D:HOH2162 2.0 8.2 1.0
O D:HOH2118 2.1 7.0 1.0
OD1 D:ASP697 2.1 11.3 1.0
O D:HOH2107 2.1 8.4 1.0
O D:HOH2144 2.1 11.6 1.0
O D:HOH2139 2.2 13.3 1.0
CG D:ASP697 3.1 10.8 1.0
OD2 D:ASP697 3.5 10.9 1.0
ZN D:ZN2002 3.9 15.4 1.0
NE2 D:HIS730 4.1 11.3 1.0
O D:HOH2125 4.1 13.3 1.0
OE2 D:GLU727 4.1 14.5 1.0
CD2 D:HIS696 4.2 11.9 1.0
O D:HOH2157 4.2 11.0 1.0
O D:HIS696 4.2 12.0 1.0
OG1 D:THR768 4.3 13.3 1.0
CD2 D:HIS700 4.3 18.1 1.0
CD2 D:HIS730 4.4 10.7 1.0
CB D:ASP697 4.5 10.8 1.0
OD2 D:ASP808 4.5 8.9 1.0
CB D:THR768 4.5 13.8 1.0
NE2 D:HIS700 4.6 18.4 1.0
NE2 D:HIS696 4.6 11.8 1.0
NE2 D:HIS656 4.6 13.0 1.0
O D:THR768 4.7 15.7 1.0
CD2 D:HIS656 4.7 12.8 1.0
CA D:ASP697 4.8 10.7 1.0
CD D:GLU727 5.0 13.4 1.0

Magnesium binding site 6 out of 8 in 5xkm

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Magnesium binding site 6 out of 8 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 6- Methyl-N-(1-(4-(Trifluoromethoxy)Phenyl)Propyl)Pyrazolo[1,5- A]Pyrimidine-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Human Phosphodiesterase 2A in Complex with 6- Methyl-N-(1-(4-(Trifluoromethoxy)Phenyl)Propyl)Pyrazolo[1,5- A]Pyrimidine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:26.3
occ:1.00
 O D:HOH2191 2.0 22.1 1.0
O D:HOH2174 2.1 34.0 1.0
O E:HOH2143 2.3 17.8 1.0
OE2 D:GLU785 2.3 33.3 1.0
O D:GLU785 2.4 24.4 1.0
CD D:GLU785 3.4 32.6 1.0
C D:GLU785 3.4 22.6 1.0
CA D:GLU785 3.9 22.9 1.0
O D:HOH2212 4.0 29.8 1.0
CG D:GLU785 4.1 29.1 1.0
O D:HOH2213 4.4 36.3 1.0
OE1 D:GLU785 4.4 32.5 1.0
O E:HOH2194 4.4 23.8 1.0
O D:HOH2168 4.4 30.4 1.0
O D:ALA784 4.5 21.7 1.0
CB D:GLU785 4.6 24.8 1.0
N D:VAL786 4.6 19.2 1.0
CA E:PRO653 4.7 17.3 1.0
O E:ARG701 4.7 20.1 1.0
OG E:SER832 4.7 35.4 1.0
CD E:PRO654 4.8 17.8 1.0
CB E:PRO653 4.9 17.6 1.0

Magnesium binding site 7 out of 8 in 5xkm

Go back to Magnesium Binding Sites List in 5xkm
Magnesium binding site 7 out of 8 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 6- Methyl-N-(1-(4-(Trifluoromethoxy)Phenyl)Propyl)Pyrazolo[1,5- A]Pyrimidine-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Human Phosphodiesterase 2A in Complex with 6- Methyl-N-(1-(4-(Trifluoromethoxy)Phenyl)Propyl)Pyrazolo[1,5- A]Pyrimidine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg2001

b:15.5
occ:1.00
 O E:HOH2172 2.0 9.5 1.0
OD1 E:ASP697 2.0 13.5 1.0
O E:HOH2102 2.1 8.4 1.0
O E:HOH2144 2.2 8.4 1.0
O E:HOH2103 2.2 11.0 1.0
O E:HOH2114 2.3 12.5 1.0
CG E:ASP697 3.1 14.8 1.0
OD2 E:ASP697 3.4 15.8 1.0
ZN E:ZN2002 3.9 19.5 1.0
OE2 E:GLU727 4.0 22.6 1.0
NE2 E:HIS730 4.0 13.6 1.0
O E:HOH2164 4.1 14.6 1.0
O E:HOH2135 4.2 12.2 1.0
OG1 E:THR768 4.2 14.9 1.0
CD2 E:HIS696 4.3 17.4 1.0
CD2 E:HIS730 4.3 13.8 1.0
O E:HIS696 4.3 16.5 1.0
CB E:ASP697 4.4 13.9 1.0
OD2 E:ASP808 4.5 12.5 1.0
CB E:THR768 4.5 16.3 1.0
CD2 E:HIS700 4.6 14.8 1.0
NE2 E:HIS656 4.6 21.2 1.0
NE2 E:HIS696 4.7 18.6 1.0
CA E:ASP697 4.8 14.3 1.0
CD2 E:HIS656 4.8 20.5 1.0
NE2 E:HIS700 4.8 16.2 1.0
CG E:GLU727 4.9 22.1 1.0
O E:THR768 4.9 19.8 1.0
CD E:GLU727 4.9 23.7 1.0

Magnesium binding site 8 out of 8 in 5xkm

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Magnesium binding site 8 out of 8 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 6- Methyl-N-(1-(4-(Trifluoromethoxy)Phenyl)Propyl)Pyrazolo[1,5- A]Pyrimidine-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Human Phosphodiesterase 2A in Complex with 6- Methyl-N-(1-(4-(Trifluoromethoxy)Phenyl)Propyl)Pyrazolo[1,5- A]Pyrimidine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2001

b:14.5
occ:1.00
 O F:HOH4001 2.0 8.5 1.0
O F:HOH4065 2.1 7.7 1.0
O F:HOH4063 2.1 7.6 1.0
OD1 F:ASP697 2.1 15.2 1.0
O F:HOH4005 2.2 13.5 1.0
O F:HOH4013 2.2 17.9 1.0
CG F:ASP697 3.1 14.5 1.0
OD2 F:ASP697 3.4 13.4 1.0
ZN F:ZN2002 3.7 17.2 1.0
O F:HOH4042 4.0 7.1 1.0
OE2 F:GLU727 4.0 26.4 1.0
CD2 F:HIS696 4.1 13.7 1.0
O F:HOH4093 4.1 15.5 1.0
OG1 F:THR768 4.2 16.8 1.0
NE2 F:HIS730 4.2 16.7 1.0
O F:HIS696 4.3 15.8 1.0
OD2 F:ASP808 4.3 12.7 1.0
CD2 F:HIS730 4.4 16.1 1.0
CB F:THR768 4.4 18.0 1.0
CB F:ASP697 4.5 13.8 1.0
NE2 F:HIS696 4.5 14.3 1.0
NE2 F:HIS656 4.6 17.8 1.0
CD2 F:HIS700 4.6 14.7 1.0
CD2 F:HIS656 4.8 17.4 1.0
O F:THR768 4.8 18.5 1.0
CA F:ASP697 4.9 13.4 1.0
NE2 F:HIS700 4.9 15.4 1.0
CG F:GLU727 4.9 22.6 1.0
CD F:GLU727 4.9 24.1 1.0

Reference:

S.Mikami, S.Sasaki, Y.Asano, O.Ujikawa, S.Fukumoto, K.Nakashima, H.Oki, N.Kamiguchi, H.Imada, H.Iwashita, T.Taniguchi. Discovery of An Orally Bioavailable, Brain-Penetrating, in Vivo Active Phosphodiesterase 2A Inhibitor Lead Series For the Treatment of Cognitive Disorders. J. Med. Chem. V. 60 7658 2017.
ISSN: ISSN 1520-4804
PubMed: 28759228
DOI: 10.1021/ACS.JMEDCHEM.7B00709
Page generated: Mon Sep 30 09:32:35 2024

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