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Sodium in PDB 5k0g: Crystal Structure of Comt in Complex with 4-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole

Enzymatic activity of Crystal Structure of Comt in Complex with 4-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole

All present enzymatic activity of Crystal Structure of Comt in Complex with 4-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole:
2.1.1.6;

Protein crystallography data

The structure of Crystal Structure of Comt in Complex with 4-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole, PDB code: 5k0g was solved by A.Ehler, R.M.Rodriguez-Sarmiento, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.37 / 1.89
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.657, 69.834, 67.372, 90.00, 106.89, 90.00
R / Rfree (%) 17.9 / 21.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Comt in Complex with 4-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole (pdb code 5k0g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Comt in Complex with 4-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole, PDB code: 5k0g:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5k0g

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Sodium binding site 1 out of 4 in the Crystal Structure of Comt in Complex with 4-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Comt in Complex with 4-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:33.5
occ:1.00
 OD1 A:ASP141 2.3 27.1 1.0
OD1 A:ASN170 2.3 29.7 1.0
OD2 A:ASP169 2.5 32.1 1.0
O A:HOH483 2.7 43.9 1.0
OD2 A:ASP141 2.9 32.1 1.0
CG A:ASP141 3.0 28.0 1.0
O A:HOH495 3.0 40.8 1.0
CG A:ASN170 3.2 29.3 1.0
CG A:ASP169 3.5 30.3 1.0
O A:HOH412 3.5 48.1 1.0
ND2 A:ASN170 3.6 27.6 1.0
CB A:ASP169 4.0 22.3 1.0
NZ A:LYS144 4.0 26.2 1.0
O A:HOH499 4.2 51.3 1.0
CG2 A:VAL42 4.3 32.9 1.0
CB A:ASP141 4.4 21.8 1.0
OD1 A:ASP169 4.5 27.2 1.0
CB A:ASN170 4.6 25.9 1.0
O A:HOH475 4.8 35.9 1.0
CA A:VAL42 4.9 36.8 1.0
N A:VAL42 5.0 39.7 1.0

Sodium binding site 2 out of 4 in 5k0g

Go back to Sodium Binding Sites List in 5k0g
Sodium binding site 2 out of 4 in the Crystal Structure of Comt in Complex with 4-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Comt in Complex with 4-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:33.9
occ:1.00
 O A:PHE189 2.2 29.3 1.0
O A:HOH497 2.3 42.3 1.0
O A:HOH489 2.4 33.0 1.0
O A:SER186 2.5 32.7 1.0
O A:VAL183 2.6 26.4 1.0
O A:ARG184 2.7 31.7 1.0
C A:ARG184 3.2 32.3 1.0
C A:PHE189 3.4 28.7 1.0
CA A:ARG184 3.6 26.6 1.0
C A:SER186 3.6 33.5 1.0
C A:VAL183 3.7 29.4 1.0
N A:SER186 3.9 29.2 1.0
N A:GLY185 4.1 29.2 1.0
N A:ARG184 4.1 25.9 1.0
CA A:PHE189 4.2 27.4 1.0
SG A:CYS191 4.2 27.2 1.0
C A:GLY185 4.2 34.4 1.0
N A:PHE189 4.2 28.3 1.0
CA A:SER186 4.3 31.1 1.0
CB A:PHE189 4.3 24.8 1.0
N A:GLU190 4.4 29.3 1.0
N A:SER187 4.6 32.1 1.0
CA A:GLY185 4.6 32.6 1.0
CA A:GLU190 4.6 31.7 1.0
O A:GLY185 4.7 36.4 1.0
N A:CYS191 4.7 29.4 1.0
CA A:SER187 4.7 31.1 1.0
CB A:ARG184 4.9 30.2 1.0
CA A:VAL183 5.0 25.5 1.0
CB A:CYS191 5.0 25.5 1.0
CB A:SER186 5.0 30.9 1.0

Sodium binding site 3 out of 4 in 5k0g

Go back to Sodium Binding Sites List in 5k0g
Sodium binding site 3 out of 4 in the Crystal Structure of Comt in Complex with 4-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Comt in Complex with 4-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:39.0
occ:1.00
 O B:PHE189 2.3 32.6 1.0
O B:SER186 2.3 35.2 1.0
O B:HOH517 2.4 45.3 1.0
O B:VAL183 2.5 27.4 1.0
O B:HOH523 2.6 34.9 1.0
O B:ARG184 2.7 32.2 1.0
C B:ARG184 3.2 31.1 1.0
C B:PHE189 3.5 29.3 1.0
C B:SER186 3.5 39.0 1.0
CA B:ARG184 3.6 30.3 1.0
C B:VAL183 3.6 28.3 1.0
N B:SER186 3.9 31.8 1.0
N B:GLY185 4.1 31.1 1.0
N B:ARG184 4.1 26.9 1.0
C B:GLY185 4.1 41.3 1.0
CA B:PHE189 4.2 31.6 1.0
N B:PHE189 4.2 29.3 1.0
CA B:SER186 4.3 32.3 1.0
SG B:CYS191 4.3 29.2 1.0
CB B:PHE189 4.3 26.3 1.0
N B:SER187 4.5 34.5 1.0
N B:GLU190 4.5 31.4 1.0
O B:GLY185 4.6 42.6 1.0
CA B:GLY185 4.6 31.2 1.0
CA B:SER187 4.6 33.4 1.0
CA B:GLU190 4.7 34.5 1.0
N B:CYS191 4.9 28.7 1.0
CB B:ARG184 4.9 31.7 1.0
CA B:VAL183 4.9 27.1 1.0
CB B:SER186 5.0 33.8 1.0
C B:SER187 5.0 32.8 1.0

Sodium binding site 4 out of 4 in 5k0g

Go back to Sodium Binding Sites List in 5k0g
Sodium binding site 4 out of 4 in the Crystal Structure of Comt in Complex with 4-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Comt in Complex with 4-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na304

b:33.8
occ:1.00
 OD1 B:ASP141 2.2 27.7 1.0
OD1 B:ASN170 2.3 32.9 1.0
OD2 B:ASP169 2.4 29.0 1.0
O B:HOH407 2.7 44.5 1.0
O B:HOH482 2.8 45.9 1.0
CG B:ASP141 2.9 30.8 1.0
OD2 B:ASP141 3.0 30.1 1.0
O B:HOH508 3.2 40.0 1.0
CG B:ASN170 3.3 32.6 1.0
CG B:ASP169 3.4 29.8 1.0
ND2 B:ASN170 3.7 27.0 1.0
CB B:ASP169 3.9 25.2 1.0
NZ B:LYS144 4.0 23.4 1.0
CG2 B:VAL42 4.2 28.1 1.0
CB B:ASP141 4.4 24.3 1.0
OD1 B:ASP169 4.4 29.9 1.0
CB B:ASN170 4.6 26.8 1.0
O B:HOH531 4.7 49.5 1.0
O B:ASP141 4.8 24.3 1.0
O B:HOH434 4.8 35.4 1.0
CA B:ASP141 5.0 25.4 1.0

Reference:

C.Lerner, R.Jakob-Roetne, B.Buettelmann, A.Ehler, M.Rudolph, R.M.Rodriguez Sarmiento. Design of Potent and Druglike Nonphenolic Inhibitors For Catechol O-Methyltransferase Derived From A Fragment Screening Approach Targeting the S-Adenosyl-L-Methionine Pocket. J. Med. Chem. V. 59 10163 2016.
ISSN: ISSN 1520-4804
PubMed: 27685665
DOI: 10.1021/ACS.JMEDCHEM.6B00927
Page generated: Tue Dec 15 11:09:22 2020

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