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Zinc 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
Magnesium (Mg) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 6 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5xkm

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Zinc binding site 1 out of 6 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 Zinc with other atoms in the Zn 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:Zn2002

b:15.2
occ:1.00
 NE2 A:HIS696 2.0 11.3 1.0
OD2 A:ASP697 2.1 10.0 1.0
NE2 A:HIS660 2.1 11.3 1.0
OD1 A:ASP808 2.1 10.4 1.0
O A:HOH2116 2.2 10.3 1.0
O A:HOH2161 2.3 12.9 1.0
CD2 A:HIS696 2.9 11.0 1.0
CE1 A:HIS696 3.0 11.2 1.0
CG A:ASP808 3.1 11.1 1.0
CG A:ASP697 3.1 10.2 1.0
CD2 A:HIS660 3.1 11.9 1.0
CE1 A:HIS660 3.1 12.2 1.0
OD2 A:ASP808 3.3 9.9 1.0
OD1 A:ASP697 3.6 10.3 1.0
MG A:MG2001 3.8 15.5 1.0
O A:HOH2124 4.0 13.0 1.0
ND1 A:HIS696 4.1 11.5 1.0
CG A:HIS696 4.1 10.8 1.0
CD2 A:HIS656 4.2 14.2 1.0
O A:HOH2115 4.2 10.0 1.0
ND1 A:HIS660 4.2 11.8 1.0
CG A:HIS660 4.3 12.0 1.0
CB A:ASP697 4.3 10.2 1.0
CB A:ASP808 4.5 11.1 1.0
NE2 A:HIS656 4.5 14.4 1.0
O A:HOH2105 4.7 13.7 1.0
CA A:ASP808 4.8 11.4 1.0
CG2 A:VAL664 4.8 13.0 1.0
O A:ASP808 4.9 11.7 1.0
O A:HOH2167 5.0 7.3 1.0

Zinc binding site 2 out of 6 in 5xkm

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Zinc binding site 2 out of 6 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 Zinc with other atoms in the Zn 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
B:Zn2002

b:17.5
occ:1.00
 NE2 B:HIS696 2.1 9.8 1.0
OD2 B:ASP697 2.1 11.5 1.0
NE2 B:HIS660 2.1 10.1 1.0
O B:HOH2110 2.2 13.4 1.0
OD1 B:ASP808 2.3 13.3 1.0
O B:HOH2132 2.4 12.0 1.0
CD2 B:HIS696 3.0 10.0 1.0
CE1 B:HIS660 3.0 10.2 1.0
CE1 B:HIS696 3.1 10.1 1.0
CG B:ASP808 3.1 13.5 1.0
CG B:ASP697 3.1 12.4 1.0
CD2 B:HIS660 3.1 10.7 1.0
OD2 B:ASP808 3.3 13.4 1.0
OD1 B:ASP697 3.6 11.9 1.0
MG B:MG2001 3.9 17.0 1.0
O B:HOH2153 4.0 8.9 1.0
CD2 B:HIS656 4.1 15.3 1.0
O B:HOH2144 4.1 13.2 1.0
ND1 B:HIS660 4.2 10.3 1.0
CG B:HIS696 4.2 10.2 1.0
ND1 B:HIS696 4.2 10.3 1.0
NE2 B:HIS656 4.2 15.6 1.0
CG B:HIS660 4.2 10.9 1.0
CB B:ASP697 4.3 11.9 1.0
CB B:ASP808 4.5 12.9 1.0
O B:HOH2106 4.7 8.6 1.0
CG2 B:VAL664 4.7 9.9 1.0
CA B:ASP808 4.9 12.2 1.0
O B:ASP808 5.0 12.1 1.0

Zinc binding site 3 out of 6 in 5xkm

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Zinc binding site 3 out of 6 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 Zinc with other atoms in the Zn 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
C:Zn2002

b:17.7
occ:1.00
 NE2 C:HIS696 2.1 11.7 1.0
OD2 C:ASP697 2.1 11.5 1.0
NE2 C:HIS660 2.2 11.4 1.0
O C:HOH2114 2.3 13.7 1.0
OD1 C:ASP808 2.3 11.5 1.0
O C:HOH2119 2.3 18.2 1.0
CD2 C:HIS696 2.9 11.7 1.0
CE1 C:HIS660 3.0 11.6 1.0
CE1 C:HIS696 3.1 11.9 1.0
CG C:ASP697 3.1 12.8 1.0
CG C:ASP808 3.2 12.5 1.0
CD2 C:HIS660 3.3 11.4 1.0
OD2 C:ASP808 3.4 12.2 1.0
OD1 C:ASP697 3.7 12.2 1.0
MG C:MG2001 3.8 15.2 1.0
O C:HOH2155 4.0 13.2 1.0
CG C:HIS696 4.1 11.7 1.0
O C:HOH2137 4.1 9.2 1.0
ND1 C:HIS696 4.2 11.3 1.0
CD2 C:HIS656 4.2 15.2 1.0
ND1 C:HIS660 4.2 11.4 1.0
NE2 C:HIS656 4.2 15.5 1.0
CB C:ASP697 4.3 12.4 1.0
CG C:HIS660 4.3 11.3 1.0
CB C:ASP808 4.6 12.4 1.0
O C:HOH2103 4.6 10.9 1.0
CG2 C:VAL664 4.8 12.5 1.0
CA C:ASP808 4.9 12.6 1.0
O C:ASP808 4.9 12.4 1.0

Zinc binding site 4 out of 6 in 5xkm

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Zinc binding site 4 out of 6 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 Zinc with other atoms in the Zn 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
D:Zn2002

b:15.4
occ:1.00
 NE2 D:HIS696 2.0 11.8 1.0
OD2 D:ASP697 2.1 10.9 1.0
NE2 D:HIS660 2.2 11.0 1.0
OD1 D:ASP808 2.2 9.2 1.0
O D:HOH2118 2.2 7.0 1.0
O D:HOH2157 2.3 11.0 1.0
CD2 D:HIS696 3.0 11.9 1.0
CE1 D:HIS660 3.0 11.5 1.0
CE1 D:HIS696 3.0 12.2 1.0
CG D:ASP697 3.1 10.8 1.0
CG D:ASP808 3.2 9.6 1.0
CD2 D:HIS660 3.2 11.3 1.0
OD2 D:ASP808 3.5 8.9 1.0
OD1 D:ASP697 3.6 11.3 1.0
MG D:MG2001 3.9 14.6 1.0
O D:HOH2139 4.1 13.3 1.0
CG D:HIS696 4.1 11.7 1.0
ND1 D:HIS696 4.1 12.3 1.0
ND1 D:HIS660 4.2 11.1 1.0
CD2 D:HIS656 4.2 12.8 1.0
O D:HOH2120 4.2 15.9 1.0
CB D:ASP697 4.3 10.8 1.0
CG D:HIS660 4.3 11.7 1.0
NE2 D:HIS656 4.5 13.0 1.0
CB D:ASP808 4.5 10.3 1.0
O D:HOH2107 4.7 8.4 1.0
CG2 D:VAL664 4.8 11.8 1.0
CA D:ASP808 4.8 10.9 1.0
O D:ASP808 5.0 12.2 1.0

Zinc binding site 5 out of 6 in 5xkm

Go back to Zinc Binding Sites List in 5xkm
Zinc binding site 5 out of 6 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 Zinc with other atoms in the Zn 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
E:Zn2002

b:19.5
occ:1.00
 OD2 E:ASP697 2.0 15.8 1.0
NE2 E:HIS660 2.1 15.2 1.0
OD1 E:ASP808 2.1 12.4 1.0
NE2 E:HIS696 2.1 18.6 1.0
O E:HOH2102 2.4 8.4 1.0
O E:HOH2135 2.4 12.2 1.0
CE1 E:HIS660 2.9 15.4 1.0
CD2 E:HIS696 3.0 17.4 1.0
CG E:ASP697 3.1 14.8 1.0
CG E:ASP808 3.1 13.1 1.0
CD2 E:HIS660 3.2 15.1 1.0
CE1 E:HIS696 3.2 17.1 1.0
OD2 E:ASP808 3.4 12.5 1.0
OD1 E:ASP697 3.6 13.5 1.0
MG E:MG2001 3.9 15.5 1.0
O E:HOH2172 4.0 9.5 1.0
ND1 E:HIS660 4.1 15.3 1.0
CD2 E:HIS656 4.1 20.5 1.0
O E:HOH2111 4.2 9.8 1.0
CG E:HIS696 4.2 17.0 1.0
CG E:HIS660 4.2 15.8 1.0
ND1 E:HIS696 4.2 16.1 1.0
CB E:ASP697 4.3 13.9 1.0
NE2 E:HIS656 4.3 21.2 1.0
CB E:ASP808 4.5 13.3 1.0
O E:ASP808 4.8 14.1 1.0
CA E:ASP808 4.8 13.5 1.0
O E:HOH2103 4.8 11.0 1.0
CG2 E:VAL664 4.8 14.8 1.0

Zinc binding site 6 out of 6 in 5xkm

Go back to Zinc Binding Sites List in 5xkm
Zinc binding site 6 out of 6 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 Zinc with other atoms in the Zn 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
F:Zn2002

b:17.2
occ:1.00
 OD2 F:ASP697 2.0 13.4 1.0
NE2 F:HIS660 2.1 16.1 1.0
NE2 F:HIS696 2.1 14.3 1.0
OD1 F:ASP808 2.2 11.8 1.0
O F:HOH4042 2.2 7.1 1.0
O F:HOH4001 2.3 8.5 1.0
CD2 F:HIS696 3.0 13.7 1.0
CE1 F:HIS660 3.1 17.1 1.0
CG F:ASP808 3.1 12.4 1.0
CD2 F:HIS660 3.1 16.8 1.0
CG F:ASP697 3.1 14.5 1.0
CE1 F:HIS696 3.2 14.0 1.0
OD2 F:ASP808 3.3 12.7 1.0
OD1 F:ASP697 3.6 15.2 1.0
MG F:MG2001 3.7 14.5 1.0
O F:HOH4065 4.0 7.7 1.0
CD2 F:HIS656 4.1 17.4 1.0
ND1 F:HIS660 4.2 17.3 1.0
CG F:HIS696 4.2 13.9 1.0
CG F:HIS660 4.2 16.7 1.0
ND1 F:HIS696 4.2 13.3 1.0
O F:HOH4004 4.3 10.7 1.0
NE2 F:HIS656 4.3 17.8 1.0
CB F:ASP697 4.3 13.8 1.0
CB F:ASP808 4.5 12.6 1.0
O F:HOH4005 4.7 13.5 1.0
O F:ASP808 4.8 13.4 1.0
CG2 F:VAL664 4.8 13.2 1.0
CA F:ASP808 4.9 12.5 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 Oct 28 15:03:49 2024

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