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Sodium in PDB 7g2j: Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm, PDB code: 7g2j was solved by M.Stihle, J.Benz, D.Hunziker, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.86 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.275, 91.714, 119.828, 90, 90, 90
R / Rfree (%) 18.2 / 22.1

Other elements in 7g2j:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Zinc (Zn) 1 atom
Chlorine (Cl) 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 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm (pdb code 7g2j). 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 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm, PDB code: 7g2j:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g2j

Go back to Sodium Binding Sites List in 7g2j
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 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 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na909

b:34.0
occ:1.00
 O A:SER804 2.3 27.2 1.0
O A:HOH1338 2.4 40.0 1.0
OG A:SER807 2.4 31.3 1.0
O A:HOH1122 2.4 29.2 1.0
O A:HOH1270 2.5 32.5 1.0
O A:ASN801 2.6 25.1 1.0
C A:ASN801 3.4 26.6 1.0
C A:SER804 3.4 27.3 1.0
CB A:SER807 3.6 30.8 1.0
CA A:ASP802 3.8 28.8 1.0
N A:ASP802 3.9 26.4 1.0
CA A:CYS805 4.1 31.6 1.0
C A:ASP802 4.2 26.4 1.0
O A:ASP802 4.2 28.1 1.0
N A:SER807 4.2 33.3 1.0
N A:CYS805 4.2 28.5 1.0
C A:CYS805 4.4 30.9 1.0
N A:SER804 4.4 26.2 1.0
CA A:SER804 4.4 26.0 1.0
CA A:SER807 4.4 34.0 1.0
CB A:ASN801 4.4 26.5 1.0
O A:CYS805 4.5 33.5 1.0
CA A:ASN801 4.5 27.3 1.0
O A:HOH1282 4.6 42.5 1.0
OD1 A:ASP802 4.6 35.5 1.0
O A:HOH1197 4.6 35.5 1.0
O A:HOH1241 4.9 41.3 1.0
CB A:SER804 4.9 27.1 1.0
N A:ASN806 4.9 33.5 1.0
N A:GLU803 5.0 24.2 1.0

Sodium binding site 2 out of 2 in 7g2j

Go back to Sodium Binding Sites List in 7g2j
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 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 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na911

b:36.4
occ:1.00
 O A:TYR669 2.2 35.3 1.0
O A:ASP672 2.3 35.9 1.0
O A:MET675 2.4 31.3 1.0
O A:HOH1324 2.4 41.0 1.0
O A:HOH1342 2.7 50.5 1.0
O A:HOH1351 2.8 52.7 1.0
C A:TYR669 3.4 35.7 1.0
C A:MET675 3.5 30.4 1.0
C A:ASP672 3.5 36.1 1.0
N A:MET675 4.2 34.2 1.0
CA A:TYR669 4.2 31.6 1.0
N A:SER676 4.4 27.4 1.0
CA A:LYS673 4.4 41.2 1.0
O A:LYS670 4.4 38.2 1.0
N A:LYS673 4.4 37.3 1.0
CA A:MET675 4.4 30.4 1.0
CA A:SER676 4.4 26.0 1.0
N A:LYS670 4.4 35.4 1.0
C A:LYS673 4.5 38.2 1.0
CA A:ASP672 4.5 35.5 1.0
CB A:TYR669 4.6 30.9 1.0
CA A:LYS670 4.6 38.1 1.0
C A:LYS670 4.6 38.3 1.0
N A:ASP672 4.6 41.4 1.0
O A:LYS673 4.7 34.2 1.0
CB A:ASP672 4.7 35.1 1.0
N A:GLN674 4.9 35.5 1.0
CB A:SER676 5.0 26.9 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 23:09:26 2025

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