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Sodium in PDB 5k0j: Crystal Structure of Comt in Complex with 5-[5-[1-(4-Methoxyphenyl) Cyclopropyl]-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) Cyclopropyl]-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) Cyclopropyl]-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) Cyclopropyl]-1H-Pyrazol-3-Yl]-2,4-Dimethyl-1,3-Thiazole, PDB code: 5k0j 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) 47.36 / 1.94
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.849, 69.666, 67.502, 90.00, 106.91, 90.00
R / Rfree (%) 19.1 / 23.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Comt in Complex with 5-[5-[1-(4-Methoxyphenyl) Cyclopropyl]-1H-Pyrazol-3-Yl]-2,4-Dimethyl-1,3-Thiazole (pdb code 5k0j). 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) Cyclopropyl]-1H-Pyrazol-3-Yl]-2,4-Dimethyl-1,3-Thiazole, PDB code: 5k0j:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5k0j

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

b:42.9
occ:1.00
 OD1 A:ASP141 2.4 29.9 1.0
OD1 A:ASN170 2.5 31.7 1.0
O A:HOH483 2.5 33.7 1.0
OD2 A:ASP169 2.8 36.3 1.0
OD2 A:ASP141 2.8 32.9 1.0
CG A:ASP141 3.0 27.6 1.0
O A:HOH485 3.2 37.0 1.0
CG A:ASN170 3.4 32.4 1.0
ND2 A:ASN170 3.6 27.5 1.0
CG A:ASP169 3.8 32.1 1.0
O A:HOH516 3.9 35.5 1.0
NZ A:LYS144 4.2 24.9 1.0
CB A:ASP169 4.3 26.2 1.0
O A:HOH484 4.4 45.6 1.0
CB A:ASP141 4.5 22.4 1.0
CG2 A:VAL42 4.6 42.6 1.0
CB A:ASN170 4.8 24.7 1.0
OD1 A:ASP169 4.8 31.5 1.0
O A:ASP141 4.8 21.8 1.0

Sodium binding site 2 out of 4 in 5k0j

Go back to Sodium Binding Sites List in 5k0j
Sodium binding site 2 out of 4 in the Crystal Structure of Comt in Complex with 5-[5-[1-(4-Methoxyphenyl) Cyclopropyl]-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) Cyclopropyl]-1H-Pyrazol-3-Yl]-2,4-Dimethyl-1,3-Thiazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:36.7
occ:1.00
 O A:PHE189 2.2 31.3 1.0
O A:SER186 2.5 33.6 1.0
O A:HOH532 2.5 37.2 1.0
O A:VAL183 2.6 25.5 1.0
O A:ARG184 2.6 34.4 1.0
O A:HOH496 2.7 42.9 1.0
C A:ARG184 3.2 34.3 1.0
C A:PHE189 3.4 28.9 1.0
C A:SER186 3.6 35.4 1.0
CA A:ARG184 3.6 28.1 1.0
C A:VAL183 3.7 30.0 1.0
N A:SER186 3.9 35.2 1.0
N A:GLY185 4.1 31.1 1.0
N A:ARG184 4.2 30.8 1.0
CA A:PHE189 4.2 30.8 1.0
SG A:CYS191 4.2 31.3 1.0
C A:GLY185 4.2 41.8 1.0
CB A:PHE189 4.3 23.8 1.0
N A:PHE189 4.3 23.7 1.0
CA A:SER186 4.3 35.4 1.0
N A:GLU190 4.4 29.3 1.0
N A:SER187 4.5 35.9 1.0
CA A:GLY185 4.6 39.8 1.0
CA A:GLU190 4.6 30.0 1.0
O A:HOH554 4.6 42.9 1.0
CA A:SER187 4.7 31.3 1.0
N A:CYS191 4.7 30.9 1.0
O A:GLY185 4.8 44.7 1.0
CA A:VAL183 5.0 26.6 1.0

Sodium binding site 3 out of 4 in 5k0j

Go back to Sodium Binding Sites List in 5k0j
Sodium binding site 3 out of 4 in the Crystal Structure of Comt in Complex with 5-[5-[1-(4-Methoxyphenyl) Cyclopropyl]-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) Cyclopropyl]-1H-Pyrazol-3-Yl]-2,4-Dimethyl-1,3-Thiazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:43.6
occ:1.00
 O B:PHE189 2.3 34.7 1.0
O B:HOH529 2.4 48.7 1.0
O B:SER186 2.5 40.0 1.0
O B:VAL183 2.5 31.9 1.0
O B:ARG184 2.6 33.4 1.0
O B:HOH548 2.8 41.7 1.0
C B:ARG184 3.1 35.4 1.0
C B:PHE189 3.4 31.1 1.0
CA B:ARG184 3.5 31.4 1.0
C B:VAL183 3.6 32.4 1.0
C B:SER186 3.6 43.7 1.0
N B:GLY185 4.0 36.6 1.0
N B:SER186 4.0 40.1 1.0
N B:ARG184 4.0 32.6 1.0
CA B:PHE189 4.2 34.3 1.0
C B:GLY185 4.2 42.7 1.0
SG B:CYS191 4.2 35.0 1.0
N B:PHE189 4.3 29.2 1.0
CB B:PHE189 4.3 22.0 1.0
CA B:SER186 4.4 36.4 1.0
N B:GLU190 4.5 35.0 1.0
CA B:GLY185 4.6 42.0 1.0
N B:SER187 4.6 42.8 1.0
CA B:GLU190 4.7 34.4 1.0
O B:GLY185 4.7 49.3 1.0
CA B:SER187 4.7 36.4 1.0
N B:CYS191 4.8 35.7 1.0
CB B:ARG184 4.8 29.9 1.0
CA B:VAL183 4.9 31.1 1.0

Sodium binding site 4 out of 4 in 5k0j

Go back to Sodium Binding Sites List in 5k0j
Sodium binding site 4 out of 4 in the Crystal Structure of Comt in Complex with 5-[5-[1-(4-Methoxyphenyl) Cyclopropyl]-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) Cyclopropyl]-1H-Pyrazol-3-Yl]-2,4-Dimethyl-1,3-Thiazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na304

b:36.7
occ:1.00
 OD1 B:ASP141 2.2 30.1 1.0
OD2 B:ASP169 2.3 31.7 1.0
OD1 B:ASN170 2.5 33.9 1.0
OD2 B:ASP141 2.6 31.5 1.0
CG B:ASP141 2.7 27.0 1.0
CG B:ASP169 3.3 33.9 1.0
CG B:ASN170 3.4 32.7 1.0
O B:HOH414 3.6 37.9 1.0
ND2 B:ASN170 3.8 27.4 1.0
CB B:ASP169 3.8 27.3 1.0
CG2 B:VAL42 4.0 35.0 1.0
O B:HOH472 4.2 32.0 1.0
CB B:ASP141 4.2 20.8 1.0
O B:HOH486 4.3 43.9 1.0
NZ B:LYS144 4.3 23.5 1.0
OD1 B:ASP169 4.4 28.5 1.0
CB B:ASN170 4.8 29.1 1.0
CA B:VAL42 4.8 36.5 1.0
O B:ASP141 4.9 23.4 1.0
CA B:ASP141 4.9 24.3 1.0
N B:VAL42 5.0 43.0 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

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