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Sodium in PDB 7g5g: Crystal Structure of Rat Autotaxin in Complex with 1-[2- (Cyclohexylmethyl)-1,3-Dioxoisoindol-4-Yl]-N-[(4-Methyl-1,2,5- Oxadiazol-3-Yl)Methyl]Piperidine-4-Carboxamide, I.E. Smiles N1(C(=O) C2C(C1=O)CCCC2N1CCC(C(=O)NCC2=Non=C2C)CC1)CC1CCCCC1 with IC50=0.0435744 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1-[2- (Cyclohexylmethyl)-1,3-Dioxoisoindol-4-Yl]-N-[(4-Methyl-1,2,5- Oxadiazol-3-Yl)Methyl]Piperidine-4-Carboxamide, I.E. Smiles N1(C(=O) C2C(C1=O)CCCC2N1CCC(C(=O)NCC2=Non=C2C)CC1)CC1CCCCC1 with IC50=0.0435744 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1-[2- (Cyclohexylmethyl)-1,3-Dioxoisoindol-4-Yl]-N-[(4-Methyl-1,2,5- Oxadiazol-3-Yl)Methyl]Piperidine-4-Carboxamide, I.E. Smiles N1(C(=O) C2C(C1=O)CCCC2N1CCC(C(=O)NCC2=Non=C2C)CC1)CC1CCCCC1 with IC50=0.0435744 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 1-[2- (Cyclohexylmethyl)-1,3-Dioxoisoindol-4-Yl]-N-[(4-Methyl-1,2,5- Oxadiazol-3-Yl)Methyl]Piperidine-4-Carboxamide, I.E. Smiles N1(C(=O) C2C(C1=O)CCCC2N1CCC(C(=O)NCC2=Non=C2C)CC1)CC1CCCCC1 with IC50=0.0435744 Microm, PDB code: 7g5g was solved by M.Stihle, J.Benz, D.Hunziker, R.Canesso, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.93 / 1.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.292, 91.86, 120.157, 90, 90, 90
R / Rfree (%) 16.6 / 22.5

Other elements in 7g5g:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1-[2- (Cyclohexylmethyl)-1,3-Dioxoisoindol-4-Yl]-N-[(4-Methyl-1,2,5- Oxadiazol-3-Yl)Methyl]Piperidine-4-Carboxamide, I.E. Smiles N1(C(=O) C2C(C1=O)CCCC2N1CCC(C(=O)NCC2=Non=C2C)CC1)CC1CCCCC1 with IC50=0.0435744 Microm also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 1-[2- (Cyclohexylmethyl)-1,3-Dioxoisoindol-4-Yl]-N-[(4-Methyl-1,2,5- Oxadiazol-3-Yl)Methyl]Piperidine-4-Carboxamide, I.E. Smiles N1(C(=O) C2C(C1=O)CCCC2N1CCC(C(=O)NCC2=Non=C2C)CC1)CC1CCCCC1 with IC50=0.0435744 Microm (pdb code 7g5g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Rat Autotaxin in Complex with 1-[2- (Cyclohexylmethyl)-1,3-Dioxoisoindol-4-Yl]-N-[(4-Methyl-1,2,5- Oxadiazol-3-Yl)Methyl]Piperidine-4-Carboxamide, I.E. Smiles N1(C(=O) C2C(C1=O)CCCC2N1CCC(C(=O)NCC2=Non=C2C)CC1)CC1CCCCC1 with IC50=0.0435744 Microm, PDB code: 7g5g:

Sodium binding site 1 out of 1 in 7g5g

Go back to Sodium Binding Sites List in 7g5g
Sodium binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with 1-[2- (Cyclohexylmethyl)-1,3-Dioxoisoindol-4-Yl]-N-[(4-Methyl-1,2,5- Oxadiazol-3-Yl)Methyl]Piperidine-4-Carboxamide, I.E. Smiles N1(C(=O) C2C(C1=O)CCCC2N1CCC(C(=O)NCC2=Non=C2C)CC1)CC1CCCCC1 with IC50=0.0435744 Microm


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 Rat Autotaxin in Complex with 1-[2- (Cyclohexylmethyl)-1,3-Dioxoisoindol-4-Yl]-N-[(4-Methyl-1,2,5- Oxadiazol-3-Yl)Methyl]Piperidine-4-Carboxamide, I.E. Smiles N1(C(=O) C2C(C1=O)CCCC2N1CCC(C(=O)NCC2=Non=C2C)CC1)CC1CCCCC1 with IC50=0.0435744 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na904

b:49.7
occ:1.00
 OG A:SER807 2.3 41.1 1.0
HG A:SER807 2.3 49.3 1.0
O A:HOH1524 2.5 52.4 1.0
O A:HOH1160 2.5 43.9 1.0
O A:SER804 2.5 43.0 1.0
O A:ASN801 2.5 40.2 1.0
O A:HOH1096 2.5 47.9 1.0
HA A:ASP802 3.1 51.8 1.0
H A:SER807 3.3 52.1 1.0
C A:ASN801 3.4 33.2 1.0
CB A:SER807 3.4 38.1 1.0
HB3 A:SER807 3.4 45.7 1.0
C A:SER804 3.5 45.8 1.0
HA A:CYS805 3.6 52.5 1.0
CA A:ASP802 3.8 43.2 1.0
N A:ASP802 4.0 33.6 1.0
H A:SER804 4.0 44.0 1.0
HB3 A:ASN801 4.0 41.2 1.0
N A:SER807 4.0 43.4 1.0
HB2 A:SER807 4.1 45.7 1.0
HB2 A:ASN801 4.1 41.2 1.0
C A:ASP802 4.2 42.5 1.0
O A:ASP802 4.2 37.1 1.0
HB2 A:SER804 4.2 49.2 1.0
CA A:CYS805 4.2 43.8 1.0
CA A:SER807 4.3 42.3 1.0
N A:CYS805 4.3 38.4 1.0
O A:HOH1299 4.3 51.4 1.0
C A:CYS805 4.3 48.4 1.0
N A:SER804 4.4 36.7 1.0
CA A:SER804 4.4 34.0 1.0
O A:CYS805 4.4 44.9 1.0
CB A:ASN801 4.4 34.3 1.0
CA A:ASN801 4.5 37.1 1.0
H A:SER808 4.6 55.1 1.0
OD1 A:ASP802 4.6 44.2 1.0
O A:HOH1245 4.7 45.7 1.0
H A:ASP802 4.7 40.3 1.0
H A:ASN801 4.8 42.2 1.0
CB A:SER804 4.8 41.0 1.0
N A:ASN806 4.8 42.9 1.0
O A:HOH1527 4.9 60.9 1.0
O A:HOH1424 4.9 51.9 1.0
N A:SER808 5.0 46.0 1.0
C A:SER807 5.0 44.9 1.0
N A:GLU803 5.0 34.6 1.0

Reference:

D.Hunziker, S.C.Joachim, C.Ullmer, M.G.Rudolph. Crystal Structure of A Rat Autotaxin Complex To Be Published.
Page generated: Sat Feb 8 23:23:00 2025

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