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Calcium in PDB 7g3j: Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[[1-Methyl-5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl) Imidazol-2-Yl]Methoxy]Benzonitrile, I.E. Smiles CLC1C(C#N)Cc(C(C)(C) C)C(C1)OCC1=Nc=C(C(=O)N2C3(CC2)COC3)N1C with IC50=0.124297 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[[1-Methyl-5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl) Imidazol-2-Yl]Methoxy]Benzonitrile, I.E. Smiles CLC1C(C#N)Cc(C(C)(C) C)C(C1)OCC1=Nc=C(C(=O)N2C3(CC2)COC3)N1C with IC50=0.124297 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[[1-Methyl-5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl) Imidazol-2-Yl]Methoxy]Benzonitrile, I.E. Smiles CLC1C(C#N)Cc(C(C)(C) C)C(C1)OCC1=Nc=C(C(=O)N2C3(CC2)COC3)N1C with IC50=0.124297 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-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl) Imidazol-2-Yl]Methoxy]Benzonitrile, I.E. Smiles CLC1C(C#N)Cc(C(C)(C) C)C(C1)OCC1=Nc=C(C(=O)N2C3(CC2)COC3)N1C with IC50=0.124297 Microm, PDB code: 7g3j was solved by M.Stihle, J.Benz, D.Hunziker, L.Green, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.95 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.287, 90.915, 117.703, 90, 90, 90
R / Rfree (%) 16.5 / 21.2

Other elements in 7g3j:

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[[1-Methyl-5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl) Imidazol-2-Yl]Methoxy]Benzonitrile, I.E. Smiles CLC1C(C#N)Cc(C(C)(C) C)C(C1)OCC1=Nc=C(C(=O)N2C3(CC2)COC3)N1C with IC50=0.124297 Microm also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom
Potassium (K) 1 atom
Sodium (Na) 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-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl) Imidazol-2-Yl]Methoxy]Benzonitrile, I.E. Smiles CLC1C(C#N)Cc(C(C)(C) C)C(C1)OCC1=Nc=C(C(=O)N2C3(CC2)COC3)N1C with IC50=0.124297 Microm (pdb code 7g3j). 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-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl) Imidazol-2-Yl]Methoxy]Benzonitrile, I.E. Smiles CLC1C(C#N)Cc(C(C)(C) C)C(C1)OCC1=Nc=C(C(=O)N2C3(CC2)COC3)N1C with IC50=0.124297 Microm, PDB code: 7g3j:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g3j

Go back to Calcium Binding Sites List in 7g3j
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-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl) Imidazol-2-Yl]Methoxy]Benzonitrile, I.E. Smiles CLC1C(C#N)Cc(C(C)(C) C)C(C1)OCC1=Nc=C(C(=O)N2C3(CC2)COC3)N1C with IC50=0.124297 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-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl) Imidazol-2-Yl]Methoxy]Benzonitrile, I.E. Smiles CLC1C(C#N)Cc(C(C)(C) C)C(C1)OCC1=Nc=C(C(=O)N2C3(CC2)COC3)N1C with IC50=0.124297 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:21.8
occ:1.00
 O A:HOH1382 2.2 24.4 1.0
OD1 A:ASP747 2.2 21.4 1.0
O A:LEU745 2.2 21.5 1.0
OD1 A:ASN741 2.2 24.8 1.0
OD1 A:ASP739 2.3 21.0 1.0
OD1 A:ASP743 2.3 22.4 1.0
CG A:ASP743 3.2 24.2 1.0
CG A:ASN741 3.3 23.8 1.0
C A:LEU745 3.4 24.1 1.0
CG A:ASP739 3.4 19.6 1.0
CG A:ASP747 3.5 22.2 1.0
OD2 A:ASP743 3.7 25.0 1.0
ND2 A:ASN741 3.8 24.8 1.0
N A:ASP747 4.0 21.5 1.0
CA A:ASP739 4.0 19.6 1.0
N A:LEU745 4.1 24.2 1.0
C A:ARG746 4.1 22.0 1.0
CA A:ASP747 4.2 22.1 1.0
CA A:LEU745 4.2 24.0 1.0
CB A:ASP739 4.3 19.2 1.0
N A:ASP743 4.3 24.2 1.0
OD2 A:ASP739 4.3 17.9 1.0
O A:ARG746 4.3 20.8 1.0
OD2 A:ASP747 4.4 23.6 1.0
CB A:ASP747 4.4 22.0 1.0
N A:ASN741 4.4 21.5 1.0
CB A:ASP743 4.4 23.1 1.0
CB A:LEU745 4.4 25.4 1.0
N A:ARG746 4.5 22.7 1.0
O A:PHE738 4.5 20.1 1.0
C A:ASP739 4.5 20.4 1.0
CB A:ASN741 4.6 20.3 1.0
OE2 A:GLU751 4.7 43.3 1.0
N A:TYR742 4.7 21.8 1.0
CA A:ASP743 4.8 22.7 1.0
N A:TYR740 4.8 20.0 1.0
CA A:ARG746 4.8 22.3 1.0
C A:ASN741 4.8 24.9 1.0
N A:GLY744 4.8 25.0 1.0
CA A:ASN741 4.8 22.0 1.0

Calcium binding site 2 out of 2 in 7g3j

Go back to Calcium Binding Sites List in 7g3j
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-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl) Imidazol-2-Yl]Methoxy]Benzonitrile, I.E. Smiles CLC1C(C#N)Cc(C(C)(C) C)C(C1)OCC1=Nc=C(C(=O)N2C3(CC2)COC3)N1C with IC50=0.124297 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-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl) Imidazol-2-Yl]Methoxy]Benzonitrile, I.E. Smiles CLC1C(C#N)Cc(C(C)(C) C)C(C1)OCC1=Nc=C(C(=O)N2C3(CC2)COC3)N1C with IC50=0.124297 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:28.8
occ:1.00
 OD1 A:ASP171 1.9 30.8 1.0
OG1 A:THR209 2.0 25.7 1.0
NE2 A:HIS359 2.2 23.6 1.0
OD2 A:ASP358 2.2 29.0 1.0
CG A:ASP171 2.7 26.2 1.0
OD2 A:ASP171 2.7 35.0 1.0
CB A:THR209 3.0 25.9 1.0
CE1 A:HIS359 3.0 25.3 1.0
CD2 A:HIS359 3.1 26.7 1.0
CG A:ASP358 3.1 27.4 1.0
CG2 A:THR209 3.4 26.8 1.0
OD1 A:ASP358 3.4 22.7 1.0
CA A:THR209 3.5 25.8 1.0
N A:THR209 3.9 25.9 1.0
CB A:ASP171 4.0 28.3 1.0
O A:HOH1415 4.0 41.7 1.0
ND1 A:HIS359 4.1 24.4 1.0
O A:HOH1102 4.1 28.1 1.0
OD1 A:ASP311 4.1 25.3 1.0
CG A:HIS359 4.1 23.4 1.0
N A:GLY172 4.3 27.2 1.0
CG A:ASP311 4.4 24.7 1.0
CA A:ASP171 4.4 26.7 1.0
CE1 A:HIS474 4.4 19.1 1.0
CB A:ASP358 4.4 24.7 1.0
ZN A:ZN1003 4.5 26.4 1.0
NE2 A:HIS474 4.6 20.9 1.0
C A:ASP171 4.7 27.0 1.0
C A:LYS208 4.7 26.1 1.0
CB A:ASP311 4.7 23.6 1.0
OH A:TYR306 4.8 33.6 1.0
OD2 A:ASP311 4.9 28.0 1.0
C A:THR209 4.9 25.0 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: Wed Jul 9 22:21:16 2025

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