Atomistry » Sodium » PDB 5jiq-5kc1 » 5k0g
Atomistry »
  Sodium »
    PDB 5jiq-5kc1 »
      5k0g »

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

Go back to Sodium Binding Sites List in 5k0g
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: Mon Oct 7 22:01:30 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy