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Sodium in PDB 7g2l: Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-C]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2CNCCC12 with IC50=0.787674 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-C]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2CNCCC12 with IC50=0.787674 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-C]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2CNCCC12 with IC50=0.787674 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-C]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2CNCCC12 with IC50=0.787674 Microm, PDB code: 7g2l 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) 45.85 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.032, 91.704, 119.464, 90, 90, 90
R / Rfree (%) 17.6 / 21.2

Other elements in 7g2l:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-C]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2CNCCC12 with IC50=0.787674 Microm also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom
Calcium (Ca) 2 atoms
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-C]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2CNCCC12 with IC50=0.787674 Microm (pdb code 7g2l). 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-C]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2CNCCC12 with IC50=0.787674 Microm, PDB code: 7g2l:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g2l

Go back to Sodium Binding Sites List in 7g2l
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-C]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2CNCCC12 with IC50=0.787674 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-C]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2CNCCC12 with IC50=0.787674 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:35.6
occ:1.00
 O A:HOH1149 2.3 29.2 1.0
O A:HOH1359 2.4 38.5 1.0
OG A:SER807 2.4 30.3 1.0
O A:SER804 2.5 27.3 1.0
O A:HOH1155 2.5 31.7 1.0
O A:ASN801 2.6 26.8 1.0
C A:ASN801 3.4 25.5 1.0
C A:SER804 3.5 27.5 1.0
CB A:SER807 3.6 30.5 1.0
CA A:ASP802 3.8 28.1 1.0
N A:ASP802 4.0 27.1 1.0
O A:ASP802 4.1 28.1 1.0
C A:ASP802 4.2 26.9 1.0
CA A:CYS805 4.2 32.6 1.0
N A:SER807 4.2 33.2 1.0
N A:CYS805 4.2 29.9 1.0
C A:CYS805 4.4 32.7 1.0
CA A:SER807 4.4 34.4 1.0
N A:SER804 4.4 25.5 1.0
CB A:ASN801 4.4 25.7 1.0
CA A:SER804 4.5 26.3 1.0
O A:HOH1177 4.5 40.3 1.0
O A:CYS805 4.5 31.3 1.0
CA A:ASN801 4.5 27.0 1.0
O A:HOH1233 4.6 37.3 1.0
OD1 A:ASP802 4.6 33.2 1.0
CB A:SER804 4.9 28.0 1.0
O A:HOH1257 4.9 34.4 1.0
N A:ASN806 4.9 33.3 1.0

Sodium binding site 2 out of 2 in 7g2l

Go back to Sodium Binding Sites List in 7g2l
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-C]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2CNCCC12 with IC50=0.787674 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-C]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2CNCCC12 with IC50=0.787674 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:34.7
occ:1.00
 O A:ASP672 2.3 32.8 1.0
O A:MET675 2.3 30.1 1.0
O A:TYR669 2.3 36.1 1.0
O A:HOH1344 2.4 42.9 1.0
C A:MET675 3.4 30.1 1.0
C A:ASP672 3.5 36.6 1.0
C A:TYR669 3.5 35.8 1.0
N A:MET675 4.0 32.2 1.0
CA A:TYR669 4.2 31.2 1.0
CA A:LYS673 4.3 39.4 1.0
N A:SER676 4.3 27.5 1.0
CA A:MET675 4.3 30.0 1.0
N A:LYS673 4.3 35.6 1.0
O A:LYS670 4.4 38.2 1.0
C A:LYS673 4.4 36.8 1.0
CA A:SER676 4.4 27.0 1.0
CA A:ASP672 4.4 34.7 1.0
N A:LYS670 4.5 37.1 1.0
O A:LYS673 4.5 37.0 1.0
N A:ASP672 4.5 41.6 1.0
CB A:TYR669 4.6 29.5 1.0
CB A:ASP672 4.6 34.5 1.0
C A:LYS670 4.7 37.5 1.0
CA A:LYS670 4.7 40.3 1.0
N A:GLN674 4.9 34.2 1.0
CB A:MET675 4.9 30.3 1.0
CB A:SER676 4.9 27.5 1.0
C A:GLN674 4.9 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 23:09:27 2025

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