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Sodium in PDB 5k0f: Crystal Structure of Comt in Complex with 5-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-2,4-Dimethyl-1,3-Thiazole

Enzymatic activity of Crystal Structure of Comt in Complex with 5-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-2,4-Dimethyl-1,3-Thiazole

All present enzymatic activity of Crystal Structure of Comt in Complex with 5-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-2,4-Dimethyl-1,3-Thiazole:
2.1.1.6;

Protein crystallography data

The structure of Crystal Structure of Comt in Complex with 5-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-2,4-Dimethyl-1,3-Thiazole, PDB code: 5k0f 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) 47.54 / 1.81
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.895, 70.096, 67.621, 90.00, 106.92, 90.00
R / Rfree (%) 17.2 / 20.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Comt in Complex with 5-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-2,4-Dimethyl-1,3-Thiazole (pdb code 5k0f). 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 5-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-2,4-Dimethyl-1,3-Thiazole, PDB code: 5k0f:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5k0f

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Sodium binding site 1 out of 4 in the Crystal Structure of Comt in Complex with 5-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-2,4-Dimethyl-1,3-Thiazole


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 5-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-2,4-Dimethyl-1,3-Thiazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:33.2
occ:1.00
 OD1 A:ASP141 2.4 26.6 1.0
OD1 A:ASN170 2.4 31.7 1.0
OD2 A:ASP169 2.5 35.0 1.0
O A:HOH525 2.8 45.3 1.0
O A:HOH493 2.9 42.2 1.0
OD2 A:ASP141 2.9 35.3 1.0
CG A:ASP141 3.0 30.5 1.0
O A:HOH484 3.1 39.2 1.0
CG A:ASN170 3.3 33.5 1.0
CG A:ASP169 3.5 33.1 1.0
ND2 A:ASN170 3.7 29.0 1.0
O A:HOH541 4.0 48.5 1.0
CB A:ASP169 4.1 22.9 1.0
NZ A:LYS144 4.2 25.0 1.0
CG2 A:VAL42 4.4 30.2 1.0
CB A:ASP141 4.5 21.8 1.0
OD1 A:ASP169 4.5 29.9 1.0
CB A:ASN170 4.7 28.4 1.0
O A:HOH477 4.7 37.0 1.0
O A:HOH550 4.9 47.8 1.0
CA A:VAL42 4.9 35.5 1.0
O A:ASP141 5.0 21.2 1.0
N A:VAL42 5.0 37.0 1.0

Sodium binding site 2 out of 4 in 5k0f

Go back to Sodium Binding Sites List in 5k0f
Sodium binding site 2 out of 4 in the Crystal Structure of Comt in Complex with 5-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-2,4-Dimethyl-1,3-Thiazole


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 5-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-2,4-Dimethyl-1,3-Thiazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:31.6
occ:1.00
 O A:PHE189 2.2 29.7 1.0
O A:HOH532 2.3 43.5 1.0
O A:SER186 2.4 31.4 1.0
O A:VAL183 2.5 27.4 1.0
O A:HOH528 2.5 32.1 1.0
O A:ARG184 2.6 32.5 1.0
C A:ARG184 3.2 33.4 1.0
C A:PHE189 3.4 28.1 1.0
C A:SER186 3.5 31.8 1.0
CA A:ARG184 3.6 26.3 1.0
C A:VAL183 3.6 28.4 1.0
N A:SER186 3.8 30.2 1.0
N A:GLY185 4.0 28.4 1.0
N A:ARG184 4.1 25.4 1.0
CA A:PHE189 4.1 29.1 1.0
C A:GLY185 4.2 37.0 1.0
CA A:SER186 4.2 31.1 1.0
N A:PHE189 4.2 27.4 1.0
SG A:CYS191 4.2 29.1 1.0
CB A:PHE189 4.2 24.1 1.0
N A:GLU190 4.4 28.5 1.0
O A:HOH538 4.5 41.0 1.0
N A:SER187 4.5 31.2 1.0
CA A:GLY185 4.6 33.5 1.0
CA A:GLU190 4.6 32.2 1.0
O A:GLY185 4.7 36.9 1.0
CA A:SER187 4.8 30.9 1.0
N A:CYS191 4.8 26.6 1.0
CA A:VAL183 4.9 26.6 1.0
CB A:SER186 4.9 36.3 1.0
CB A:ARG184 5.0 29.5 1.0

Sodium binding site 3 out of 4 in 5k0f

Go back to Sodium Binding Sites List in 5k0f
Sodium binding site 3 out of 4 in the Crystal Structure of Comt in Complex with 5-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-2,4-Dimethyl-1,3-Thiazole


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 5-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-2,4-Dimethyl-1,3-Thiazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:36.9
occ:1.00
 O B:PHE189 2.3 36.6 1.0
O B:HOH528 2.3 44.2 1.0
O B:SER186 2.4 33.9 1.0
O B:VAL183 2.4 27.0 1.0
O B:ARG184 2.6 32.3 1.0
O B:HOH536 2.7 33.3 1.0
C B:ARG184 3.1 32.5 1.0
C B:PHE189 3.4 28.7 1.0
CA B:ARG184 3.5 26.0 1.0
C B:SER186 3.5 38.8 1.0
C B:VAL183 3.5 27.9 1.0
N B:SER186 3.8 31.5 1.0
N B:ARG184 4.0 28.0 1.0
N B:GLY185 4.0 28.8 1.0
C B:GLY185 4.1 40.4 1.0
CA B:PHE189 4.2 31.1 1.0
CA B:SER186 4.2 31.7 1.0
SG B:CYS191 4.2 30.4 1.0
CB B:PHE189 4.3 24.9 1.0
N B:PHE189 4.3 29.5 1.0
N B:GLU190 4.5 30.0 1.0
N B:SER187 4.5 37.0 1.0
CA B:GLY185 4.6 33.4 1.0
O B:GLY185 4.7 40.4 1.0
CA B:SER187 4.7 35.7 1.0
CA B:GLU190 4.7 35.6 1.0
CA B:VAL183 4.8 26.3 1.0
CB B:ARG184 4.8 32.6 1.0
CB B:SER186 4.9 36.1 1.0
N B:CYS191 4.9 31.1 1.0

Sodium binding site 4 out of 4 in 5k0f

Go back to Sodium Binding Sites List in 5k0f
Sodium binding site 4 out of 4 in the Crystal Structure of Comt in Complex with 5-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-2,4-Dimethyl-1,3-Thiazole


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 5-[5-[1-(4-Methoxyphenyl) Ethyl]-1H-Pyrazol-3-Yl]-2,4-Dimethyl-1,3-Thiazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na304

b:34.2
occ:1.00
 OD1 B:ASN170 2.3 29.3 1.0
OD1 B:ASP141 2.3 31.4 1.0
O B:HOH491 2.4 45.6 1.0
OD2 B:ASP169 2.4 30.4 1.0
O B:HOH499 2.7 42.6 1.0
O B:HOH526 3.0 40.9 1.0
CG B:ASP141 3.0 30.1 1.0
OD2 B:ASP141 3.1 30.9 1.0
CG B:ASN170 3.3 33.7 1.0
CG B:ASP169 3.4 32.4 1.0
ND2 B:ASN170 3.7 27.8 1.0
CB B:ASP169 3.9 22.6 1.0
NZ B:LYS144 4.1 25.9 1.0
OD1 B:ASP169 4.3 29.1 1.0
CG2 B:VAL42 4.4 26.9 1.0
O B:HOH538 4.4 42.2 1.0
CB B:ASP141 4.5 22.7 1.0
O B:HOH408 4.5 49.7 1.0
CB B:ASN170 4.6 27.9 1.0
O B:HOH432 4.8 40.6 1.0
O B:ASP141 4.9 22.5 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 22:01:23 2024

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