Atomistry » Zinc » PDB 5xgw-5xwi » 5xkm
Atomistry »
  Zinc »
    PDB 5xgw-5xwi »
      5xkm »

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

Go back to Zinc Binding Sites List in 5xkm
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

Go back to Zinc Binding Sites List in 5xkm
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

Go back to Zinc Binding Sites List in 5xkm
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

Go back to Zinc Binding Sites List in 5xkm
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: Wed Dec 16 11:20:35 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy