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Calcium in PDB 7g3u: Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[[1-Methyl-5-[5-(Oxetan-3-Yl)-1,2-Oxazol-3-Yl]Imidazol-2- Yl]Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C(N1C)C1=Noc(=C1)C1COC1)Cl)C#N with IC50=0.0167757 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[[1-Methyl-5-[5-(Oxetan-3-Yl)-1,2-Oxazol-3-Yl]Imidazol-2- Yl]Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C(N1C)C1=Noc(=C1)C1COC1)Cl)C#N with IC50=0.0167757 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[[1-Methyl-5-[5-(Oxetan-3-Yl)-1,2-Oxazol-3-Yl]Imidazol-2- Yl]Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C(N1C)C1=Noc(=C1)C1COC1)Cl)C#N with IC50=0.0167757 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[[1-Methyl-5-[5-(Oxetan-3-Yl)-1,2-Oxazol-3-Yl]Imidazol-2- Yl]Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C(N1C)C1=Noc(=C1)C1COC1)Cl)C#N with IC50=0.0167757 Microm, PDB code: 7g3u was solved by M.Stihle, J.Benz, D.Hunziker, D.Mazunin, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.32 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.526, 92.589, 121.142, 90, 90, 90
R / Rfree (%) 18.4 / 23.2

Other elements in 7g3u:

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[[1-Methyl-5-[5-(Oxetan-3-Yl)-1,2-Oxazol-3-Yl]Imidazol-2- Yl]Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C(N1C)C1=Noc(=C1)C1COC1)Cl)C#N with IC50=0.0167757 Microm also contains other interesting chemical elements:

Sodium (Na) 1 atom
Chlorine (Cl) 3 atoms
Zinc (Zn) 1 atom
Potassium (K) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[[1-Methyl-5-[5-(Oxetan-3-Yl)-1,2-Oxazol-3-Yl]Imidazol-2- Yl]Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C(N1C)C1=Noc(=C1)C1COC1)Cl)C#N with IC50=0.0167757 Microm (pdb code 7g3u). 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- Chloro-4-[[1-Methyl-5-[5-(Oxetan-3-Yl)-1,2-Oxazol-3-Yl]Imidazol-2- Yl]Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C(N1C)C1=Noc(=C1)C1COC1)Cl)C#N with IC50=0.0167757 Microm, PDB code: 7g3u:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g3u

Go back to Calcium Binding Sites List in 7g3u
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[[1-Methyl-5-[5-(Oxetan-3-Yl)-1,2-Oxazol-3-Yl]Imidazol-2- Yl]Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C(N1C)C1=Noc(=C1)C1COC1)Cl)C#N with IC50=0.0167757 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- Chloro-4-[[1-Methyl-5-[5-(Oxetan-3-Yl)-1,2-Oxazol-3-Yl]Imidazol-2- Yl]Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C(N1C)C1=Noc(=C1)C1COC1)Cl)C#N with IC50=0.0167757 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:18.2
occ:1.00
 OD1 A:ASP747 2.3 19.1 1.0
OD1 A:ASP739 2.3 17.7 1.0
O A:LEU745 2.3 16.4 1.0
OD1 A:ASP743 2.3 20.4 1.0
OD1 A:ASN741 2.4 18.8 1.0
O A:HOH1469 2.4 21.5 1.0
CG A:ASP743 3.3 19.5 1.0
CG A:ASP739 3.5 18.4 1.0
CG A:ASN741 3.5 24.6 1.0
C A:LEU745 3.5 16.8 1.0
CG A:ASP747 3.5 17.9 1.0
OD2 A:ASP743 3.7 23.1 1.0
CA A:ASP739 3.9 18.4 1.0
N A:ASP747 3.9 15.5 1.0
ND2 A:ASN741 4.0 26.3 1.0
N A:LEU745 4.1 16.9 1.0
C A:ARG746 4.1 15.6 1.0
CB A:ASP739 4.1 17.1 1.0
CA A:ASP747 4.2 17.4 1.0
CA A:LEU745 4.2 16.7 1.0
N A:ASP743 4.3 18.2 1.0
O A:ARG746 4.3 15.2 1.0
OD2 A:ASP739 4.4 17.8 1.0
CB A:ASP747 4.4 18.7 1.0
O A:PHE738 4.4 17.3 1.0
OD2 A:ASP747 4.4 21.0 1.0
N A:ASN741 4.4 20.2 1.0
CB A:LEU745 4.5 18.1 1.0
C A:ASP739 4.5 19.8 1.0
O A:HOH1213 4.5 27.1 1.0
CB A:ASP743 4.5 18.3 1.0
N A:ARG746 4.5 16.4 1.0
OE2 A:GLU751 4.6 31.2 1.0
CB A:ASN741 4.7 20.7 1.0
N A:TYR742 4.8 17.3 1.0
N A:TYR740 4.8 19.6 1.0
CA A:ASP743 4.8 16.7 1.0
CA A:ARG746 4.8 16.9 1.0
C A:ASN741 4.9 20.5 1.0
CA A:ASN741 4.9 23.1 1.0
N A:GLY744 4.9 16.0 1.0

Calcium binding site 2 out of 2 in 7g3u

Go back to Calcium Binding Sites List in 7g3u
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[[1-Methyl-5-[5-(Oxetan-3-Yl)-1,2-Oxazol-3-Yl]Imidazol-2- Yl]Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C(N1C)C1=Noc(=C1)C1COC1)Cl)C#N with IC50=0.0167757 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- Chloro-4-[[1-Methyl-5-[5-(Oxetan-3-Yl)-1,2-Oxazol-3-Yl]Imidazol-2- Yl]Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C(N1C)C1=Noc(=C1)C1COC1)Cl)C#N with IC50=0.0167757 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:50.7
occ:1.00
 OD1 A:ASP171 1.8 25.6 1.0
OG1 A:THR209 1.9 24.9 1.0
NE2 A:HIS359 2.1 16.2 1.0
OD2 A:ASP358 2.6 24.6 1.0
CG A:ASP171 2.7 21.4 1.0
CE1 A:HIS359 2.9 16.3 1.0
CB A:THR209 2.9 20.4 1.0
OD2 A:ASP171 3.0 29.9 1.0
CG2 A:THR209 3.1 22.2 1.0
O A:HOH1027 3.1 28.9 1.0
CD2 A:HIS359 3.1 15.8 1.0
CA A:THR209 3.4 18.8 1.0
CG A:ASP358 3.4 22.3 1.0
OD1 A:ASP358 3.5 19.5 1.0
OD1 A:ASP311 3.8 19.9 1.0
O3 A:SO4909 3.9 35.3 1.0
N A:THR209 3.9 17.8 1.0
ND1 A:HIS359 4.0 14.6 1.0
CB A:ASP171 4.0 16.6 1.0
O A:HOH1013 4.1 22.4 1.0
CG A:HIS359 4.2 15.3 1.0
CG A:ASP311 4.2 16.3 1.0
CE1 A:HIS474 4.2 20.6 1.0
N A:GLY172 4.3 18.0 1.0
CA A:ASP171 4.4 17.6 1.0
ZN A:ZN901 4.4 21.6 1.0
NE2 A:HIS474 4.4 17.5 1.0
OD2 A:ASP311 4.7 20.3 1.0
CB A:ASP358 4.7 19.8 1.0
C A:LYS208 4.7 17.6 1.0
CB A:ASP311 4.7 17.7 1.0
C A:THR209 4.7 19.9 1.0
C A:ASP171 4.8 16.5 1.0
O1 A:SO4909 4.8 80.2 1.0
OH A:TYR306 4.9 30.9 1.0
S A:SO4909 5.0 74.5 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 15:39:43 2025

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