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Sodium in PDB 5k0c: Crystal Structure of Comt in Complex with 2,4-Dimethyl-5-[3-(2- Phenylpropan-2-Yl)-1H-Pyrazol-5-Yl]-1,3-Thiazole

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

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

Protein crystallography data

The structure of Crystal Structure of Comt in Complex with 2,4-Dimethyl-5-[3-(2- Phenylpropan-2-Yl)-1H-Pyrazol-5-Yl]-1,3-Thiazole, PDB code: 5k0c 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) 45.78 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.141, 70.064, 67.762, 90.00, 106.69, 90.00
R / Rfree (%) 17.6 / 23.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Comt in Complex with 2,4-Dimethyl-5-[3-(2- Phenylpropan-2-Yl)-1H-Pyrazol-5-Yl]-1,3-Thiazole (pdb code 5k0c). 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 2,4-Dimethyl-5-[3-(2- Phenylpropan-2-Yl)-1H-Pyrazol-5-Yl]-1,3-Thiazole, PDB code: 5k0c:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5k0c

Go back to Sodium Binding Sites List in 5k0c
Sodium binding site 1 out of 4 in the Crystal Structure of Comt in Complex with 2,4-Dimethyl-5-[3-(2- Phenylpropan-2-Yl)-1H-Pyrazol-5-Yl]-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 2,4-Dimethyl-5-[3-(2- Phenylpropan-2-Yl)-1H-Pyrazol-5-Yl]-1,3-Thiazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:35.8
occ:1.00
 OD1 A:ASP141 2.3 27.4 1.0
OD1 A:ASN170 2.3 34.6 1.0
OD2 A:ASP169 2.5 34.8 1.0
O A:HOH535 2.5 44.3 1.0
O A:HOH539 2.9 35.7 1.0
CG A:ASP141 3.0 28.1 1.0
OD2 A:ASP141 3.0 32.9 1.0
CG A:ASN170 3.3 29.1 1.0
O A:HOH531 3.4 47.2 1.0
CG A:ASP169 3.5 31.1 1.0
ND2 A:ASN170 3.6 27.3 1.0
CB A:ASP169 4.1 22.9 1.0
NZ A:LYS144 4.1 27.6 1.0
O A:HOH455 4.3 36.7 1.0
CG2 A:VAL42 4.4 28.4 1.0
CB A:ASP141 4.5 20.9 1.0
OD1 A:ASP169 4.5 28.8 1.0
CB A:ASN170 4.7 25.4 1.0
O A:ASP141 4.9 22.6 1.0

Sodium binding site 2 out of 4 in 5k0c

Go back to Sodium Binding Sites List in 5k0c
Sodium binding site 2 out of 4 in the Crystal Structure of Comt in Complex with 2,4-Dimethyl-5-[3-(2- Phenylpropan-2-Yl)-1H-Pyrazol-5-Yl]-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 2,4-Dimethyl-5-[3-(2- Phenylpropan-2-Yl)-1H-Pyrazol-5-Yl]-1,3-Thiazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na306

b:32.9
occ:1.00
 O A:PHE189 2.2 30.1 1.0
O A:HOH545 2.4 45.7 1.0
O A:SER186 2.4 29.9 1.0
O A:VAL183 2.5 26.3 1.0
O A:HOH540 2.5 34.6 1.0
O A:ARG184 2.7 32.5 1.0
C A:ARG184 3.2 32.8 1.0
C A:PHE189 3.4 29.2 1.0
C A:SER186 3.6 31.3 1.0
C A:VAL183 3.6 29.4 1.0
CA A:ARG184 3.6 27.0 1.0
N A:SER186 3.9 30.4 1.0
N A:GLY185 4.1 30.2 1.0
N A:ARG184 4.1 28.6 1.0
CA A:PHE189 4.1 29.1 1.0
SG A:CYS191 4.2 27.0 1.0
CB A:PHE189 4.2 22.9 1.0
N A:PHE189 4.2 24.0 1.0
O A:HOH557 4.3 37.9 1.0
CA A:SER186 4.3 29.9 1.0
C A:GLY185 4.3 38.0 1.0
N A:GLU190 4.4 28.9 1.0
N A:SER187 4.6 33.0 1.0
CA A:GLU190 4.6 30.5 1.0
CA A:GLY185 4.6 32.3 1.0
N A:CYS191 4.8 30.5 1.0
CA A:SER187 4.8 30.4 1.0
CA A:VAL183 4.9 29.2 1.0
CB A:CYS191 4.9 24.1 1.0
O A:GLY185 4.9 37.5 1.0
CB A:ARG184 5.0 31.7 1.0
CB A:SER186 5.0 29.0 1.0

Sodium binding site 3 out of 4 in 5k0c

Go back to Sodium Binding Sites List in 5k0c
Sodium binding site 3 out of 4 in the Crystal Structure of Comt in Complex with 2,4-Dimethyl-5-[3-(2- Phenylpropan-2-Yl)-1H-Pyrazol-5-Yl]-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 2,4-Dimethyl-5-[3-(2- Phenylpropan-2-Yl)-1H-Pyrazol-5-Yl]-1,3-Thiazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:41.7
occ:1.00
 O B:HOH541 2.3 43.6 1.0
O B:PHE189 2.3 35.9 1.0
O B:SER186 2.5 37.8 1.0
O B:ARG184 2.6 32.2 1.0
O B:VAL183 2.6 27.0 1.0
O B:HOH561 2.6 38.8 1.0
C B:ARG184 3.2 32.7 1.0
C B:PHE189 3.5 33.9 1.0
CA B:ARG184 3.6 31.6 1.0
C B:SER186 3.6 40.3 1.0
C B:VAL183 3.7 30.3 1.0
N B:SER186 4.0 34.7 1.0
N B:GLY185 4.1 33.8 1.0
N B:ARG184 4.1 28.6 1.0
SG B:CYS191 4.2 32.7 1.0
C B:GLY185 4.3 42.7 1.0
CA B:PHE189 4.3 34.8 1.0
CA B:SER186 4.4 34.3 1.0
O B:HOH577 4.4 47.4 1.0
N B:PHE189 4.4 28.5 1.0
CB B:PHE189 4.4 25.4 1.0
N B:GLU190 4.5 33.0 1.0
CA B:GLY185 4.6 33.1 1.0
N B:SER187 4.6 41.2 1.0
CA B:GLU190 4.7 32.5 1.0
O B:GLY185 4.8 41.0 1.0
CA B:SER187 4.8 33.9 1.0
N B:CYS191 4.9 31.0 1.0
CB B:ARG184 4.9 31.7 1.0

Sodium binding site 4 out of 4 in 5k0c

Go back to Sodium Binding Sites List in 5k0c
Sodium binding site 4 out of 4 in the Crystal Structure of Comt in Complex with 2,4-Dimethyl-5-[3-(2- Phenylpropan-2-Yl)-1H-Pyrazol-5-Yl]-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 2,4-Dimethyl-5-[3-(2- Phenylpropan-2-Yl)-1H-Pyrazol-5-Yl]-1,3-Thiazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na304

b:36.8
occ:1.00
 OD1 B:ASP141 2.3 26.6 1.0
OD1 B:ASN170 2.4 27.5 1.0
OD2 B:ASP169 2.7 29.2 1.0
O B:HOH498 3.0 37.2 1.0
CG B:ASP141 3.1 30.4 1.0
OD2 B:ASP141 3.2 28.9 1.0
CG B:ASN170 3.4 33.6 1.0
CG B:ASP169 3.6 29.9 1.0
ND2 B:ASN170 3.8 29.5 1.0
O B:HOH442 4.0 38.8 1.0
O B:HOH551 4.0 42.2 1.0
NZ B:LYS144 4.1 23.2 1.0
CB B:ASP169 4.1 22.3 1.0
CG2 B:VAL42 4.4 25.8 1.0
CB B:ASP141 4.6 19.8 1.0
OD1 B:ASP169 4.6 28.8 1.0
CB B:ASN170 4.7 27.6 1.0
O B:ASP141 4.8 22.8 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 22:00:27 2024

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