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Magnesium in PDB 5k0n: Crystal Structure of Comt in Complex with 4-[5-[1-(4-Methoxyphenyl) Cyclopropyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole

Enzymatic activity of Crystal Structure of Comt in Complex with 4-[5-[1-(4-Methoxyphenyl) Cyclopropyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole

All present enzymatic activity of Crystal Structure of Comt in Complex with 4-[5-[1-(4-Methoxyphenyl) Cyclopropyl]-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) Cyclopropyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole, PDB code: 5k0n was solved by A.Ehler, R.M.Rodriguez-Sarmiento, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.42 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.023, 69.890, 104.102, 90.00, 94.09, 90.00
R / Rfree (%) 18.4 / 23.3

Other elements in 5k0n:

The structure of Crystal Structure of Comt in Complex with 4-[5-[1-(4-Methoxyphenyl) Cyclopropyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole 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 4-[5-[1-(4-Methoxyphenyl) Cyclopropyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole (pdb code 5k0n). 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 4-[5-[1-(4-Methoxyphenyl) Cyclopropyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole, PDB code: 5k0n:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5k0n

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Magnesium binding site 1 out of 4 in the Crystal Structure of Comt in Complex with 4-[5-[1-(4-Methoxyphenyl) Cyclopropyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole


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 4-[5-[1-(4-Methoxyphenyl) Cyclopropyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:41.2
occ:1.00
 O A:HOH402 2.0 39.3 1.0
OD1 A:ASN170 2.1 36.1 1.0
O A:HOH422 2.2 39.3 1.0
OD1 A:ASN41 2.2 37.0 1.0
OD1 A:ASP141 2.3 28.8 1.0
CG A:ASP141 3.1 30.9 1.0
CG A:ASN170 3.3 34.4 1.0
CG A:ASN41 3.3 36.9 1.0
OD2 A:ASP141 3.3 37.3 1.0
O A:HOH521 3.3 39.6 1.0
NZ A:LYS144 3.5 29.6 1.0
OD2 A:ASP169 3.7 42.1 1.0
ND2 A:ASN170 3.8 26.8 1.0
N A:ASN41 4.0 33.0 1.0
ND2 A:ASN41 4.0 29.9 1.0
CA A:ASN41 4.1 37.5 1.0
O A:HOH529 4.1 50.7 1.0
CB A:ASN41 4.3 31.7 1.0
O A:ASP141 4.3 23.3 1.0
CE A:LYS144 4.5 32.7 1.0
CB A:ASN170 4.5 29.8 1.0
CB A:ASP141 4.5 23.6 1.0
O A:HOH512 4.6 45.9 1.0
CG A:ASP169 4.6 32.4 1.0
CB A:ASP169 4.9 23.7 1.0
CA A:ASP141 4.9 24.1 1.0
C A:ASP141 4.9 24.1 1.0
CG A:MET40 5.0 42.2 1.0

Magnesium binding site 2 out of 4 in 5k0n

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Magnesium binding site 2 out of 4 in the Crystal Structure of Comt in Complex with 4-[5-[1-(4-Methoxyphenyl) Cyclopropyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole


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 4-[5-[1-(4-Methoxyphenyl) Cyclopropyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:35.2
occ:1.00
 O B:HOH402 2.1 40.6 1.0
O B:HOH419 2.2 37.2 1.0
O B:HOH516 2.2 44.5 1.0
OD1 B:ASN41 2.3 29.3 1.0
OD1 B:ASP141 2.3 28.1 1.0
OD1 B:ASN170 2.3 36.2 1.0
OD2 B:ASP141 2.7 30.1 1.0
CG B:ASP141 2.8 25.4 1.0
CG B:ASN41 3.2 31.7 1.0
CG B:ASN170 3.4 32.9 1.0
NZ B:LYS144 3.8 24.2 1.0
N B:ASN41 3.8 28.4 1.0
CA B:ASN41 3.8 35.6 1.0
O B:HOH540 3.9 48.9 1.0
ND2 B:ASN170 4.0 27.8 1.0
ND2 B:ASN41 4.0 28.9 1.0
OD2 B:ASP169 4.1 34.6 1.0
CB B:ASN41 4.1 32.2 1.0
CB B:ASP141 4.3 22.0 1.0
O B:ASP141 4.4 23.9 1.0
O B:HOH401 4.7 36.6 1.0
CE B:LYS144 4.7 26.5 1.0
CB B:ASN170 4.7 31.3 1.0
CG B:ASP169 4.7 32.0 1.0
O B:HOH504 4.8 51.4 1.0
CA B:ASP141 4.9 22.4 1.0
CB B:ASP169 4.9 24.1 1.0
C B:MET40 5.0 35.7 1.0
C B:ASP141 5.0 19.8 1.0
CB B:MET40 5.0 32.2 1.0

Magnesium binding site 3 out of 4 in 5k0n

Go back to Magnesium Binding Sites List in 5k0n
Magnesium binding site 3 out of 4 in the Crystal Structure of Comt in Complex with 4-[5-[1-(4-Methoxyphenyl) Cyclopropyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole


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 4-[5-[1-(4-Methoxyphenyl) Cyclopropyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:34.7
occ:1.00
 O C:HOH401 2.1 39.1 1.0
O C:HOH415 2.2 36.0 1.0
OD1 C:ASN41 2.2 27.2 1.0
OD1 C:ASP141 2.2 25.7 1.0
OD1 C:ASN170 2.4 31.1 1.0
OD2 C:ASP141 2.6 28.2 1.0
O1 C:NHE302 2.6 42.4 1.0
CG C:ASP141 2.7 23.0 1.0
CG C:ASN41 3.2 31.8 1.0
CG C:ASN170 3.5 27.0 1.0
S C:NHE302 3.7 42.6 1.0
C2 C:NHE302 3.7 37.6 1.0
OD2 C:ASP169 3.7 34.0 1.0
CA C:ASN41 3.8 32.5 1.0
N C:ASN41 3.9 30.7 1.0
NZ C:LYS144 3.9 22.6 1.0
ND2 C:ASN41 3.9 26.2 1.0
CB C:ASN41 4.1 28.6 1.0
ND2 C:ASN170 4.1 23.5 1.0
CB C:ASP141 4.2 20.9 1.0
O3 C:NHE302 4.4 40.4 1.0
O C:ASP141 4.4 21.0 1.0
CG C:ASP169 4.5 32.3 1.0
CB C:ASN170 4.7 28.3 1.0
CB C:ASP169 4.7 24.5 1.0
CE C:LYS144 4.8 25.6 1.0
CA C:ASP141 4.9 21.7 1.0
O2 C:NHE302 4.9 44.7 1.0

Magnesium binding site 4 out of 4 in 5k0n

Go back to Magnesium Binding Sites List in 5k0n
Magnesium binding site 4 out of 4 in the Crystal Structure of Comt in Complex with 4-[5-[1-(4-Methoxyphenyl) Cyclopropyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole


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 4-[5-[1-(4-Methoxyphenyl) Cyclopropyl]-1H-Pyrazol-3-Yl]-1,3-Dimethylpyrazole within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:29.4
occ:1.00
 O D:HOH406 2.1 32.7 1.0
OD1 D:ASN41 2.2 27.6 1.0
O D:HOH423 2.2 30.7 1.0
OD1 D:ASN170 2.3 27.9 1.0
O3 D:NHE303 2.4 34.1 1.0
OD1 D:ASP141 2.4 23.9 1.0
CG D:ASP141 3.2 21.5 1.0
CG D:ASN41 3.2 27.9 1.0
OD2 D:ASP141 3.2 27.2 1.0
CG D:ASN170 3.4 25.5 1.0
S D:NHE303 3.6 32.2 1.0
NZ D:LYS144 3.7 21.0 1.0
C2 D:NHE303 3.8 29.8 1.0
ND2 D:ASN170 3.9 24.1 1.0
N D:ASN41 3.9 22.9 1.0
CA D:ASN41 4.0 26.6 1.0
ND2 D:ASN41 4.0 23.2 1.0
CB D:ASN41 4.2 24.8 1.0
O1 D:NHE303 4.3 36.5 1.0
OD2 D:ASP169 4.4 35.3 1.0
O D:ASP141 4.5 21.5 1.0
CE D:LYS144 4.6 26.2 1.0
CB D:ASP141 4.6 18.8 1.0
CB D:ASN170 4.6 24.9 1.0
O2 D:NHE303 4.8 36.2 1.0
CG D:ASP169 4.8 28.4 1.0
O D:HOH559 4.8 38.8 1.0
CB D:MET40 5.0 29.9 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: Sun Sep 29 18:49:52 2024

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