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Sodium in PDB 7g3d: Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm, PDB code: 7g3d 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) 48.83 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.23, 91.79, 119.85, 90, 90, 90
R / Rfree (%) 17.7 / 21.8

Other elements in 7g3d:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm (pdb code 7g3d). 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-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm, PDB code: 7g3d:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g3d

Go back to Sodium Binding Sites List in 7g3d
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 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-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na910

b:34.4
occ:1.00
 OG A:SER807 2.3 26.2 1.0
O A:HOH1394 2.3 39.1 1.0
O A:SER804 2.4 27.1 1.0
O A:HOH1125 2.4 29.7 1.0
O A:HOH1329 2.4 33.8 1.0
O A:ASN801 2.5 25.4 1.0
C A:ASN801 3.4 24.9 1.0
C A:SER804 3.4 27.2 1.0
CB A:SER807 3.5 28.1 1.0
CA A:ASP802 3.9 28.3 1.0
N A:ASP802 4.0 26.7 1.0
O A:ASP802 4.1 26.7 1.0
N A:SER807 4.1 30.1 1.0
C A:ASP802 4.2 26.9 1.0
CA A:CYS805 4.2 31.6 1.0
N A:CYS805 4.2 28.1 1.0
CA A:SER807 4.3 29.4 1.0
O A:HOH1100 4.3 40.1 1.0
CB A:ASN801 4.4 25.7 1.0
C A:CYS805 4.4 31.6 1.0
N A:SER804 4.4 25.4 1.0
CA A:SER804 4.4 26.8 1.0
CA A:ASN801 4.4 26.2 1.0
O A:CYS805 4.5 29.0 1.0
O A:HOH1240 4.7 38.2 1.0
OD1 A:ASP802 4.7 33.7 1.0
CB A:SER804 4.8 29.0 1.0
N A:ASN806 4.9 31.2 1.0
O A:HOH1292 4.9 36.9 1.0
N A:GLU803 5.0 24.4 1.0

Sodium binding site 2 out of 2 in 7g3d

Go back to Sodium Binding Sites List in 7g3d
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 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-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na912

b:32.9
occ:1.00
 O A:TYR669 2.3 33.5 1.0
O A:MET675 2.3 29.4 1.0
O A:ASP672 2.4 37.7 1.0
O A:HOH1385 2.4 52.5 1.0
O A:HOH1338 2.4 44.3 1.0
O A:HOH1411 2.9 52.0 1.0
C A:TYR669 3.4 33.9 1.0
C A:MET675 3.5 28.4 1.0
C A:ASP672 3.5 36.4 1.0
N A:MET675 4.2 30.6 1.0
CA A:TYR669 4.2 30.4 1.0
N A:SER676 4.3 25.2 1.0
O A:LYS670 4.3 39.4 1.0
CA A:MET675 4.4 29.1 1.0
CA A:SER676 4.4 24.6 1.0
CA A:LYS673 4.4 38.6 1.0
O A:HOH1429 4.4 49.6 1.0
N A:LYS673 4.4 37.2 1.0
N A:LYS670 4.4 34.4 1.0
CA A:ASP672 4.5 35.5 1.0
C A:LYS673 4.5 35.7 1.0
N A:ASP672 4.5 39.4 1.0
O A:LYS673 4.6 33.1 1.0
CB A:TYR669 4.6 29.3 1.0
C A:LYS670 4.6 34.5 1.0
CA A:LYS670 4.6 36.1 1.0
CB A:ASP672 4.7 35.0 1.0
CB A:SER676 4.9 25.8 1.0
N A:GLN674 5.0 33.0 1.0
CB A:MET675 5.0 29.6 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 23:12:39 2025

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