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Sodium in PDB 7g5b: Crystal Structure of Rat Autotaxin in Complex with N-[5-[2-(4- Fluorophenyl)Ethynyl]Pyridin-2-Yl]Acetamide, I.E. Smiles C(#CC1CCC(F)CC1)C1CNC(Nc(=O)C)CC1 with IC50=1.56678 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with N-[5-[2-(4- Fluorophenyl)Ethynyl]Pyridin-2-Yl]Acetamide, I.E. Smiles C(#CC1CCC(F)CC1)C1CNC(Nc(=O)C)CC1 with IC50=1.56678 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with N-[5-[2-(4- Fluorophenyl)Ethynyl]Pyridin-2-Yl]Acetamide, I.E. Smiles C(#CC1CCC(F)CC1)C1CNC(Nc(=O)C)CC1 with IC50=1.56678 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with N-[5-[2-(4- Fluorophenyl)Ethynyl]Pyridin-2-Yl]Acetamide, I.E. Smiles C(#CC1CCC(F)CC1)C1CNC(Nc(=O)C)CC1 with IC50=1.56678 Microm, PDB code: 7g5b was solved by M.Stihle, J.Benz, D.Hunziker, H.Stadler, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.97 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.992, 91.617, 120.549, 90, 90, 90
R / Rfree (%) 19.3 / 23.6

Other elements in 7g5b:

The structure of Crystal Structure of Rat Autotaxin in Complex with N-[5-[2-(4- Fluorophenyl)Ethynyl]Pyridin-2-Yl]Acetamide, I.E. Smiles C(#CC1CCC(F)CC1)C1CNC(Nc(=O)C)CC1 with IC50=1.56678 Microm also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with N-[5-[2-(4- Fluorophenyl)Ethynyl]Pyridin-2-Yl]Acetamide, I.E. Smiles C(#CC1CCC(F)CC1)C1CNC(Nc(=O)C)CC1 with IC50=1.56678 Microm (pdb code 7g5b). 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 N-[5-[2-(4- Fluorophenyl)Ethynyl]Pyridin-2-Yl]Acetamide, I.E. Smiles C(#CC1CCC(F)CC1)C1CNC(Nc(=O)C)CC1 with IC50=1.56678 Microm, PDB code: 7g5b:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g5b

Go back to Sodium Binding Sites List in 7g5b
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with N-[5-[2-(4- Fluorophenyl)Ethynyl]Pyridin-2-Yl]Acetamide, I.E. Smiles C(#CC1CCC(F)CC1)C1CNC(Nc(=O)C)CC1 with IC50=1.56678 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 N-[5-[2-(4- Fluorophenyl)Ethynyl]Pyridin-2-Yl]Acetamide, I.E. Smiles C(#CC1CCC(F)CC1)C1CNC(Nc(=O)C)CC1 with IC50=1.56678 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na903

b:33.3
occ:1.00
 O A:MET675 2.2 29.9 1.0
O A:ASP672 2.3 29.8 1.0
O A:TYR669 2.4 28.4 1.0
O A:HOH1390 2.5 34.9 1.0
O A:HOH1266 2.6 45.5 1.0
O A:HOH1393 3.0 41.7 1.0
C A:MET675 3.3 27.6 1.0
C A:ASP672 3.5 30.8 1.0
C A:TYR669 3.5 31.0 1.0
N A:SER676 4.1 22.2 1.0
N A:MET675 4.2 29.9 1.0
CA A:SER676 4.2 24.0 1.0
CA A:MET675 4.3 26.3 1.0
CA A:TYR669 4.3 27.2 1.0
CA A:LYS673 4.3 37.2 1.0
C A:LYS673 4.3 32.3 1.0
N A:LYS673 4.3 32.7 1.0
O A:LYS673 4.4 31.5 1.0
O A:LYS670 4.5 34.5 1.0
CB A:TYR669 4.5 25.5 1.0
CA A:ASP672 4.5 31.8 1.0
N A:LYS670 4.6 30.6 1.0
N A:ASP672 4.7 37.4 1.0
CB A:SER676 4.7 21.2 1.0
CB A:ASP672 4.7 30.9 1.0
CA A:LYS670 4.8 32.2 1.0
C A:LYS670 4.8 31.7 1.0
N A:GLN674 4.8 33.5 1.0
C A:GLN674 5.0 36.9 1.0

Sodium binding site 2 out of 2 in 7g5b

Go back to Sodium Binding Sites List in 7g5b
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with N-[5-[2-(4- Fluorophenyl)Ethynyl]Pyridin-2-Yl]Acetamide, I.E. Smiles C(#CC1CCC(F)CC1)C1CNC(Nc(=O)C)CC1 with IC50=1.56678 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 N-[5-[2-(4- Fluorophenyl)Ethynyl]Pyridin-2-Yl]Acetamide, I.E. Smiles C(#CC1CCC(F)CC1)C1CNC(Nc(=O)C)CC1 with IC50=1.56678 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:50.1
occ:1.00
 O A:ASN650 2.4 36.2 1.0
O A:HOH1387 2.4 46.0 1.0
O A:THR567 2.5 31.7 1.0
O A:HOH1346 2.5 33.8 1.0
O A:HOH1399 2.6 45.2 1.0
OG1 A:THR567 2.6 37.9 1.0
C A:ASN650 3.2 35.3 1.0
C A:THR567 3.3 37.9 1.0
N A:THR567 3.7 37.7 1.0
CB A:THR567 3.7 41.5 1.0
O A:HOH1294 3.8 50.0 1.0
CA A:THR567 3.8 35.8 1.0
CB A:ASN650 3.8 38.6 1.0
N A:CYS651 4.0 30.4 1.0
CA A:CYS651 4.0 31.9 1.0
CA A:ASN650 4.1 39.8 1.0
O A:HOH1185 4.2 48.8 1.0
N A:VAL652 4.2 22.9 1.0
N A:CYS568 4.4 32.2 1.0
C A:CYS651 4.5 27.8 1.0
CA A:CYS568 4.8 37.9 1.0
C A:CYS566 4.9 41.9 1.0
CG2 A:THR567 4.9 37.6 1.0
O A:HOH1139 4.9 40.5 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 23:20:50 2025

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