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Sodium in PDB 7g6r: Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-N-Methyl-3-Nitrobenzamide, I.E. Smiles C1(=Cn(C2C1CCCN2)CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)Nc with IC50=0.0467384 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-N-Methyl-3-Nitrobenzamide, I.E. Smiles C1(=Cn(C2C1CCCN2)CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)Nc with IC50=0.0467384 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-N-Methyl-3-Nitrobenzamide, I.E. Smiles C1(=Cn(C2C1CCCN2)CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)Nc with IC50=0.0467384 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-N-Methyl-3-Nitrobenzamide, I.E. Smiles C1(=Cn(C2C1CCCN2)CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)Nc with IC50=0.0467384 Microm, PDB code: 7g6r was solved by M.Stihle, J.Benz, D.Hunziker, E.Martin-Rainer, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.87 / 1.61
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.722, 91.73, 119.255, 90, 90, 90
R / Rfree (%) 19.6 / 22.6

Other elements in 7g6r:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-N-Methyl-3-Nitrobenzamide, I.E. Smiles C1(=Cn(C2C1CCCN2)CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)Nc with IC50=0.0467384 Microm also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-N-Methyl-3-Nitrobenzamide, I.E. Smiles C1(=Cn(C2C1CCCN2)CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)Nc with IC50=0.0467384 Microm (pdb code 7g6r). 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 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-N-Methyl-3-Nitrobenzamide, I.E. Smiles C1(=Cn(C2C1CCCN2)CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)Nc with IC50=0.0467384 Microm, PDB code: 7g6r:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g6r

Go back to Sodium Binding Sites List in 7g6r
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-N-Methyl-3-Nitrobenzamide, I.E. Smiles C1(=Cn(C2C1CCCN2)CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)Nc with IC50=0.0467384 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 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-N-Methyl-3-Nitrobenzamide, I.E. Smiles C1(=Cn(C2C1CCCN2)CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)Nc with IC50=0.0467384 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:21.4
occ:1.00
 OG A:SER807 2.2 18.8 1.0
O A:HOH1470 2.3 27.2 1.0
O A:SER804 2.4 16.6 1.0
O A:HOH1298 2.4 24.5 1.0
O A:HOH1330 2.5 24.4 1.0
O A:ASN801 2.6 19.1 1.0
C A:ASN801 3.4 19.7 1.0
CB A:SER807 3.4 19.9 1.0
C A:SER804 3.5 18.4 1.0
CA A:ASP802 3.9 19.9 1.0
N A:ASP802 4.0 18.9 1.0
N A:SER807 4.1 22.2 1.0
CA A:CYS805 4.2 21.8 1.0
O A:ASP802 4.2 16.4 1.0
C A:ASP802 4.3 18.1 1.0
CA A:SER807 4.3 22.4 1.0
N A:CYS805 4.3 18.4 1.0
O A:HOH1118 4.3 32.5 1.0
C A:CYS805 4.3 21.9 1.0
N A:SER804 4.4 15.8 1.0
CB A:ASN801 4.4 18.2 1.0
CA A:ASN801 4.4 17.2 1.0
CA A:SER804 4.4 16.0 1.0
O A:CYS805 4.4 24.0 1.0
O A:HOH1101 4.6 29.3 1.0
OD1 A:ASP802 4.7 29.1 1.0
CB A:SER804 4.7 15.9 1.0
N A:ASN806 4.8 21.6 1.0
O A:HOH1383 4.9 32.8 1.0
C A:SER807 5.0 24.1 1.0

Sodium binding site 2 out of 2 in 7g6r

Go back to Sodium Binding Sites List in 7g6r
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-N-Methyl-3-Nitrobenzamide, I.E. Smiles C1(=Cn(C2C1CCCN2)CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)Nc with IC50=0.0467384 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 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-N-Methyl-3-Nitrobenzamide, I.E. Smiles C1(=Cn(C2C1CCCN2)CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)Nc with IC50=0.0467384 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:24.1
occ:1.00
 O A:MET675 2.3 22.4 1.0
O A:TYR669 2.3 22.2 1.0
O A:ASP672 2.3 24.0 1.0
O A:HOH1452 2.4 27.7 1.0
O A:HOH1495 2.6 40.8 1.0
C A:MET675 3.4 21.0 1.0
C A:TYR669 3.4 24.5 1.0
C A:ASP672 3.5 23.8 1.0
N A:MET675 4.0 24.0 1.0
CA A:TYR669 4.2 19.4 1.0
N A:SER676 4.3 17.8 1.0
CA A:MET675 4.3 22.1 1.0
CA A:LYS673 4.3 28.1 1.0
O A:LYS670 4.4 31.4 1.0
N A:LYS673 4.4 25.9 1.0
CA A:ASP672 4.4 23.5 1.0
CA A:SER676 4.4 17.6 1.0
N A:LYS670 4.4 23.8 1.0
C A:LYS673 4.4 25.8 1.0
N A:ASP672 4.4 24.9 1.0
O A:HOH1525 4.4 41.3 1.0
O A:LYS673 4.6 27.2 1.0
CA A:LYS670 4.6 29.6 1.0
CB A:ASP672 4.6 24.5 1.0
CB A:TYR669 4.6 19.1 1.0
C A:LYS670 4.6 28.6 1.0
N A:GLN674 4.9 23.4 1.0
CB A:SER676 4.9 18.3 1.0
CB A:MET675 4.9 21.2 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 23:30:33 2025

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