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Sodium in PDB 7g35: Crystal Structure of Rat Autotaxin in Complex with 3-(2,4- Dichlorophenyl)-N-[(4S)-2-[2-(Methylamino)-2-Oxoethyl]-3-Oxo-4,5- Dihydro-1H-2-Benzazepin-4-Yl]Propanamide, I.E. Smiles C1CCCC2C1C[C@@H](C(=O)N(C2)Cc(=O)Nc)Nc(=O)CCC1C(Cc(CC1)Cl)Cl with IC50=1.93883 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-(2,4- Dichlorophenyl)-N-[(4S)-2-[2-(Methylamino)-2-Oxoethyl]-3-Oxo-4,5- Dihydro-1H-2-Benzazepin-4-Yl]Propanamide, I.E. Smiles C1CCCC2C1C[C@@H](C(=O)N(C2)Cc(=O)Nc)Nc(=O)CCC1C(Cc(CC1)Cl)Cl with IC50=1.93883 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-(2,4- Dichlorophenyl)-N-[(4S)-2-[2-(Methylamino)-2-Oxoethyl]-3-Oxo-4,5- Dihydro-1H-2-Benzazepin-4-Yl]Propanamide, I.E. Smiles C1CCCC2C1C[C@@H](C(=O)N(C2)Cc(=O)Nc)Nc(=O)CCC1C(Cc(CC1)Cl)Cl with IC50=1.93883 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-(2,4- Dichlorophenyl)-N-[(4S)-2-[2-(Methylamino)-2-Oxoethyl]-3-Oxo-4,5- Dihydro-1H-2-Benzazepin-4-Yl]Propanamide, I.E. Smiles C1CCCC2C1C[C@@H](C(=O)N(C2)Cc(=O)Nc)Nc(=O)CCC1C(Cc(CC1)Cl)Cl with IC50=1.93883 Microm, PDB code: 7g35 was solved by M.Stihle, J.Benz, D.Hunziker, H.Kuhne, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.03 / 1.67
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.238, 92.07, 118.985, 90, 90, 90
R / Rfree (%) 19.3 / 23.1

Other elements in 7g35:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-(2,4- Dichlorophenyl)-N-[(4S)-2-[2-(Methylamino)-2-Oxoethyl]-3-Oxo-4,5- Dihydro-1H-2-Benzazepin-4-Yl]Propanamide, I.E. Smiles C1CCCC2C1C[C@@H](C(=O)N(C2)Cc(=O)Nc)Nc(=O)CCC1C(Cc(CC1)Cl)Cl with IC50=1.93883 Microm also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Zinc (Zn) 1 atom
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 3-(2,4- Dichlorophenyl)-N-[(4S)-2-[2-(Methylamino)-2-Oxoethyl]-3-Oxo-4,5- Dihydro-1H-2-Benzazepin-4-Yl]Propanamide, I.E. Smiles C1CCCC2C1C[C@@H](C(=O)N(C2)Cc(=O)Nc)Nc(=O)CCC1C(Cc(CC1)Cl)Cl with IC50=1.93883 Microm (pdb code 7g35). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Rat Autotaxin in Complex with 3-(2,4- Dichlorophenyl)-N-[(4S)-2-[2-(Methylamino)-2-Oxoethyl]-3-Oxo-4,5- Dihydro-1H-2-Benzazepin-4-Yl]Propanamide, I.E. Smiles C1CCCC2C1C[C@@H](C(=O)N(C2)Cc(=O)Nc)Nc(=O)CCC1C(Cc(CC1)Cl)Cl with IC50=1.93883 Microm, PDB code: 7g35:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g35

Go back to Sodium Binding Sites List in 7g35
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-(2,4- Dichlorophenyl)-N-[(4S)-2-[2-(Methylamino)-2-Oxoethyl]-3-Oxo-4,5- Dihydro-1H-2-Benzazepin-4-Yl]Propanamide, I.E. Smiles C1CCCC2C1C[C@@H](C(=O)N(C2)Cc(=O)Nc)Nc(=O)CCC1C(Cc(CC1)Cl)Cl with IC50=1.93883 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 3-(2,4- Dichlorophenyl)-N-[(4S)-2-[2-(Methylamino)-2-Oxoethyl]-3-Oxo-4,5- Dihydro-1H-2-Benzazepin-4-Yl]Propanamide, I.E. Smiles C1CCCC2C1C[C@@H](C(=O)N(C2)Cc(=O)Nc)Nc(=O)CCC1C(Cc(CC1)Cl)Cl with IC50=1.93883 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na904

b:23.8
occ:1.00
 OG A:SER807 2.3 20.5 1.0
O A:HOH1543 2.3 29.3 1.0
O A:SER804 2.4 17.2 1.0
O A:HOH1284 2.5 24.9 1.0
O A:ASN801 2.5 16.3 1.0
O A:HOH1327 2.5 26.6 1.0
C A:ASN801 3.4 16.3 1.0
C A:SER804 3.5 16.4 1.0
CB A:SER807 3.5 19.8 1.0
CA A:ASP802 3.8 17.6 1.0
N A:ASP802 4.0 16.6 1.0
N A:SER807 4.1 21.8 1.0
CA A:CYS805 4.2 18.3 1.0
C A:ASP802 4.2 17.2 1.0
O A:ASP802 4.2 18.0 1.0
N A:CYS805 4.2 18.4 1.0
CA A:SER807 4.3 22.2 1.0
CB A:ASN801 4.3 16.5 1.0
N A:SER804 4.3 14.0 1.0
C A:CYS805 4.3 21.2 1.0
O A:HOH1175 4.3 33.5 1.0
CA A:ASN801 4.4 14.5 1.0
O A:CYS805 4.4 23.2 1.0
CA A:SER804 4.4 14.1 1.0
OD1 A:ASP802 4.6 24.4 1.0
O A:HOH1228 4.7 30.1 1.0
O A:HOH1206 4.7 31.9 1.0
CB A:SER804 4.7 13.0 1.0
N A:ASN806 4.9 21.4 1.0
C A:SER807 5.0 24.8 1.0

Sodium binding site 2 out of 2 in 7g35

Go back to Sodium Binding Sites List in 7g35
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-(2,4- Dichlorophenyl)-N-[(4S)-2-[2-(Methylamino)-2-Oxoethyl]-3-Oxo-4,5- Dihydro-1H-2-Benzazepin-4-Yl]Propanamide, I.E. Smiles C1CCCC2C1C[C@@H](C(=O)N(C2)Cc(=O)Nc)Nc(=O)CCC1C(Cc(CC1)Cl)Cl with IC50=1.93883 Microm


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 Rat Autotaxin in Complex with 3-(2,4- Dichlorophenyl)-N-[(4S)-2-[2-(Methylamino)-2-Oxoethyl]-3-Oxo-4,5- Dihydro-1H-2-Benzazepin-4-Yl]Propanamide, I.E. Smiles C1CCCC2C1C[C@@H](C(=O)N(C2)Cc(=O)Nc)Nc(=O)CCC1C(Cc(CC1)Cl)Cl with IC50=1.93883 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:24.1
occ:1.00
 O A:MET675 2.2 22.5 1.0
O A:ASP672 2.3 23.7 1.0
O A:TYR669 2.3 25.9 1.0
O A:HOH1420 2.4 28.1 1.0
O A:HOH1564 2.8 37.5 1.0
C A:MET675 3.4 20.6 1.0
C A:TYR669 3.5 25.1 1.0
C A:ASP672 3.5 24.1 1.0
N A:MET675 4.0 23.1 1.0
CA A:TYR669 4.2 22.4 1.0
CA A:MET675 4.3 20.2 1.0
O A:LYS670 4.3 30.6 1.0
N A:SER676 4.3 17.2 1.0
O A:HOH1600 4.4 38.1 1.0
CA A:LYS673 4.4 25.6 1.0
N A:LYS673 4.4 24.1 1.0
CA A:ASP672 4.4 24.1 1.0
CA A:SER676 4.4 16.4 1.0
N A:ASP672 4.4 24.6 1.0
C A:LYS673 4.4 24.2 1.0
N A:LYS670 4.5 25.1 1.0
CB A:ASP672 4.5 21.9 1.0
C A:LYS670 4.5 25.8 1.0
CA A:LYS670 4.6 26.8 1.0
O A:LYS673 4.6 28.1 1.0
CB A:TYR669 4.6 22.9 1.0
N A:GLN674 4.8 23.1 1.0
CB A:MET675 4.9 20.8 1.0
C A:GLN674 5.0 25.1 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 23:12:39 2025

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