Magnesium in PDB 5k0l: 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: 5k0l 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) 45.44 / 2.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.167, 69.963, 104.053, 90.00, 94.18, 90.00
R / Rfree (%) 19.8 / 24.9

Other elements in 5k0l:

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 also contains other interesting chemical elements:

Potassium (K) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 5k0l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium 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: 5k0l:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5k0l

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg301

b:33.4
occ:1.00
 OD1 A:ASN170 2.1 31.3 1.0
O A:HOH482 2.2 44.2 1.0
OD1 A:ASN41 2.2 34.2 1.0
OD1 A:ASP141 2.4 26.7 1.0
CG A:ASP141 3.1 27.8 1.0
OD2 A:ASP141 3.1 33.5 1.0
CG A:ASN170 3.2 33.2 1.0
CG A:ASN41 3.3 34.2 1.0
OD2 A:ASP169 3.4 43.0 1.0
ND2 A:ASN170 3.6 24.6 1.0
CA A:ASN41 3.8 32.6 1.0
N A:ASN41 3.9 29.9 1.0
CG A:ASP169 4.1 34.2 1.0
CB A:ASN41 4.2 30.5 1.0
NZ A:LYS144 4.2 26.7 1.0
ND2 A:ASN41 4.2 29.1 1.0
CB A:ASN170 4.5 30.2 1.0
CB A:ASP169 4.5 27.7 1.0
CB A:ASP141 4.6 22.0 1.0
O A:ASP141 4.7 23.9 1.0
OD1 A:ASP169 4.9 31.2 1.0

Magnesium binding site 2 out of 4 in 5k0l

Go back to Magnesium Binding Sites List in 5k0l
Magnesium 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 Magnesium with other atoms in the Mg 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
B:Mg301

b:34.0
occ:1.00
 O B:HOH428 2.2 38.1 1.0
OD1 B:ASN41 2.2 25.5 1.0
O B:HOH498 2.2 41.5 1.0
OD1 B:ASN170 2.3 27.7 1.0
OD1 B:ASP141 2.3 28.1 1.0
OD2 B:ASP141 2.7 35.9 1.0
CG B:ASP141 2.8 24.6 1.0
CG B:ASN41 3.2 29.2 1.0
CG B:ASN170 3.3 27.0 1.0
OD2 B:ASP169 3.8 34.9 1.0
ND2 B:ASN170 3.8 24.2 1.0
CA B:ASN41 3.9 32.6 1.0
N B:ASN41 3.9 26.9 1.0
NZ B:LYS144 4.0 26.0 1.0
ND2 B:ASN41 4.0 24.3 1.0
CB B:ASN41 4.1 30.1 1.0
O B:HOH540 4.2 42.0 1.0
CB B:ASP141 4.3 24.3 1.0
CG B:ASP169 4.5 28.6 1.0
O B:ASP141 4.5 20.3 1.0
CB B:ASN170 4.6 25.2 1.0
O B:HOH410 4.8 37.5 1.0
CB B:ASP169 4.8 22.7 1.0
CE B:LYS144 4.9 25.9 1.0
O B:HOH525 5.0 48.0 1.0

Magnesium binding site 3 out of 4 in 5k0l

Go back to Magnesium Binding Sites List in 5k0l
Magnesium 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 Magnesium with other atoms in the Mg 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
C:Mg301

b:31.1
occ:1.00
 O C:HOH401 2.1 35.9 1.0
OD1 C:ASP141 2.2 26.1 1.0
OD1 C:ASN41 2.3 29.1 1.0
OD1 C:ASN170 2.3 32.8 1.0
OD2 C:ASP141 2.5 31.4 1.0
CG C:ASP141 2.7 25.4 1.0
O2 C:NHE303 2.7 42.0 1.0
O C:HOH434 3.1 35.0 1.0
CG C:ASN41 3.1 29.2 1.0
OD2 C:ASP169 3.4 35.5 1.0
CG C:ASN170 3.5 30.1 1.0
S C:NHE303 3.8 43.1 1.0
CA C:ASN41 3.8 33.6 1.0
NZ C:LYS144 3.9 24.3 1.0
ND2 C:ASN41 3.9 29.1 1.0
C2 C:NHE303 4.0 39.5 1.0
ND2 C:ASN170 4.0 25.7 1.0
N C:ASN41 4.0 29.9 1.0
CB C:ASN41 4.0 29.6 1.0
CG C:ASP169 4.1 30.5 1.0
CB C:ASP141 4.2 20.0 1.0
O3 C:NHE303 4.3 37.1 1.0
O C:ASP141 4.5 19.9 1.0
CB C:ASP169 4.5 23.4 1.0
CB C:ASN170 4.7 25.9 1.0
O C:HOH433 4.8 40.3 1.0
CA C:ASP141 4.9 21.2 1.0
O1 C:NHE303 4.9 42.2 1.0
CE C:LYS144 4.9 29.2 1.0
O C:HOH525 5.0 39.3 1.0

Magnesium binding site 4 out of 4 in 5k0l

Go back to Magnesium Binding Sites List in 5k0l
Magnesium 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 Magnesium with other atoms in the Mg 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
D:Mg301

b:30.2
occ:1.00
 O D:HOH402 2.1 32.5 1.0
OD1 D:ASN170 2.1 28.3 1.0
O D:HOH434 2.2 30.7 1.0
OD1 D:ASN41 2.2 26.8 1.0
OD1 D:ASP141 2.4 23.6 1.0
O3 D:NHE303 2.5 37.1 1.0
CG D:ASP141 3.2 21.8 1.0
CG D:ASN170 3.3 25.3 1.0
CG D:ASN41 3.3 28.6 1.0
OD2 D:ASP141 3.4 26.0 1.0
S D:NHE303 3.6 35.2 1.0
NZ D:LYS144 3.6 20.9 1.0
C2 D:NHE303 3.8 29.4 1.0
ND2 D:ASN170 3.8 24.8 1.0
N D:ASN41 4.0 22.9 1.0
CA D:ASN41 4.0 26.6 1.0
ND2 D:ASN41 4.1 22.9 1.0
OD2 D:ASP169 4.2 30.6 1.0
CB D:ASN41 4.3 24.8 1.0
O1 D:NHE303 4.3 32.1 1.0
O D:ASP141 4.4 20.7 1.0
CB D:ASN170 4.5 25.8 1.0
CE D:LYS144 4.6 25.4 1.0
CB D:ASP141 4.6 20.6 1.0
CG D:ASP169 4.7 28.4 1.0
O2 D:NHE303 4.8 36.0 1.0
O D:HOH543 4.8 36.6 1.0
CB D:ASP169 4.9 23.3 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 Dec 14 20:36:40 2020

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