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Calcium in PDB 7g3a: Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm, PDB code: 7g3a was solved by M.Stihle, J.Benz, D.Hunziker, H.Richter, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.91 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.858, 91.826, 119.462, 90, 90, 90
R / Rfree (%) 18.8 / 22.6

Other elements in 7g3a:

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm (pdb code 7g3a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm, PDB code: 7g3a:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g3a

Go back to Calcium Binding Sites List in 7g3a
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:26.8
occ:1.00
 OG1 A:THR209 1.8 21.5 1.0
OD1 A:ASP171 2.0 24.5 1.0
NE2 A:HIS359 2.1 16.4 1.0
OD2 A:ASP358 2.3 24.6 1.0
CG A:ASP171 2.6 23.0 1.0
OD2 A:ASP171 2.6 32.8 1.0
O A:HOH1063 2.7 43.4 1.0
CE1 A:HIS359 3.0 15.9 1.0
CB A:THR209 3.0 18.2 1.0
CD2 A:HIS359 3.1 16.4 1.0
CG A:ASP358 3.2 23.3 1.0
CG2 A:THR209 3.3 19.8 1.0
CA A:THR209 3.5 17.0 1.0
OD1 A:ASP358 3.5 21.7 1.0
N A:THR209 3.8 16.6 1.0
CB A:ASP171 4.0 20.4 1.0
OD1 A:ASP311 4.0 21.8 1.0
ND1 A:HIS359 4.1 16.7 1.0
O A:HOH1009 4.2 30.7 1.0
CG A:HIS359 4.2 16.4 1.0
CE1 A:HIS474 4.2 18.4 1.0
CG A:ASP311 4.3 20.7 1.0
N A:GLY172 4.3 16.0 1.0
ZN A:ZN905 4.3 21.9 1.0
CA A:ASP171 4.4 18.7 1.0
NE2 A:HIS474 4.4 18.1 1.0
CB A:ASP358 4.6 20.4 1.0
C A:ASP171 4.7 18.9 1.0
CB A:ASP311 4.7 18.6 1.0
OD2 A:ASP311 4.7 22.0 1.0
C A:LYS208 4.7 17.9 1.0
O A:HOH1403 4.7 35.0 1.0
C A:THR209 4.8 17.3 1.0
OH A:TYR306 4.9 28.5 1.0

Calcium binding site 2 out of 2 in 7g3a

Go back to Calcium Binding Sites List in 7g3a
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:18.5
occ:1.00
 OD1 A:ASN741 2.3 19.6 1.0
OD1 A:ASP743 2.3 23.2 1.0
OD1 A:ASP747 2.3 20.7 1.0
OD1 A:ASP739 2.3 17.3 1.0
O A:HOH1371 2.3 19.5 1.0
O A:LEU745 2.3 17.8 1.0
CG A:ASP743 3.3 20.1 1.0
CG A:ASN741 3.4 22.1 1.0
C A:LEU745 3.5 17.8 1.0
CG A:ASP739 3.5 16.9 1.0
CG A:ASP747 3.6 19.5 1.0
OD2 A:ASP743 3.7 22.0 1.0
ND2 A:ASN741 3.8 22.2 1.0
CA A:ASP739 3.9 16.2 1.0
N A:ASP747 4.0 19.0 1.0
N A:LEU745 4.1 16.8 1.0
C A:ARG746 4.1 18.3 1.0
O A:ARG746 4.2 16.5 1.0
CA A:LEU745 4.2 16.9 1.0
CB A:ASP739 4.2 15.2 1.0
CA A:ASP747 4.2 18.8 1.0
N A:ASP743 4.2 18.1 1.0
OD2 A:ASP747 4.4 21.7 1.0
C A:ASP739 4.4 17.0 1.0
OD2 A:ASP739 4.4 16.2 1.0
CB A:LEU745 4.5 17.6 1.0
N A:ASN741 4.5 17.9 1.0
N A:ARG746 4.5 17.2 1.0
CB A:ASP743 4.5 19.1 1.0
CB A:ASP747 4.5 17.6 1.0
O A:PHE738 4.5 15.2 1.0
OE2 A:GLU751 4.6 32.0 1.0
N A:TYR740 4.7 16.8 1.0
CB A:ASN741 4.7 19.5 1.0
N A:TYR742 4.7 17.9 1.0
CA A:ARG746 4.7 17.6 1.0
CA A:ASP743 4.8 17.4 1.0
O A:HOH1383 4.8 34.9 1.0
C A:ASN741 4.8 20.1 1.0
N A:GLY744 4.9 18.2 1.0
CA A:ASN741 4.9 19.2 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 15:35:20 2025

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