Atomistry » Calcium » PDB 7g2r-7g3u » 7g3e
Atomistry »
  Calcium »
    PDB 7g2r-7g3u »
      7g3e »

Calcium in PDB 7g3e: Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 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-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 Microm, PDB code: 7g3e was solved by M.Stihle, J.Benz, D.Hunziker, E.Pinard, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.82 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.939, 91.59, 120.062, 90, 90, 90
R / Rfree (%) 17.4 / 20.7

Other elements in 7g3e:

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 Microm also contains other interesting chemical elements:

Sodium (Na) 1 atom
Zinc (Zn) 1 atom
Chlorine (Cl) 2 atoms
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- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 Microm (pdb code 7g3e). 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-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 Microm, PDB code: 7g3e:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g3e

Go back to Calcium Binding Sites List in 7g3e
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 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-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:32.8
occ:1.00
 OG1 A:THR209 1.8 26.9 1.0
OD1 A:ASP171 1.9 30.4 1.0
NE2 A:HIS359 2.1 24.2 1.0
OD2 A:ASP358 2.4 32.6 1.0
O A:HOH1013 2.6 44.7 1.0
CG A:ASP171 2.6 27.9 1.0
OD2 A:ASP171 2.7 35.8 1.0
CB A:THR209 2.9 24.5 1.0
CE1 A:HIS359 3.0 24.1 1.0
CD2 A:HIS359 3.1 24.4 1.0
CG2 A:THR209 3.2 30.1 1.0
CG A:ASP358 3.3 28.2 1.0
CA A:THR209 3.5 24.5 1.0
OD1 A:ASP358 3.5 24.6 1.0
N A:THR209 3.9 24.3 1.0
CB A:ASP171 4.0 26.0 1.0
OD1 A:ASP311 4.1 29.5 1.0
ND1 A:HIS359 4.1 23.4 1.0
CG A:HIS359 4.2 23.4 1.0
CE1 A:HIS474 4.2 26.9 1.0
CG A:ASP311 4.4 28.2 1.0
N A:GLY172 4.4 24.9 1.0
O A:HOH1001 4.4 30.0 1.0
ZN A:ZN907 4.4 28.0 1.0
CA A:ASP171 4.4 26.1 1.0
NE2 A:HIS474 4.4 25.5 1.0
O A:HOH1339 4.5 36.0 1.0
CB A:ASP358 4.6 25.4 1.0
C A:ASP171 4.7 25.4 1.0
C A:LYS208 4.7 26.7 1.0
OD2 A:ASP311 4.8 35.0 1.0
CB A:ASP311 4.8 27.0 1.0
C A:THR209 4.8 26.4 1.0

Calcium binding site 2 out of 2 in 7g3e

Go back to Calcium Binding Sites List in 7g3e
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 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-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca909

b:23.3
occ:1.00
 OD1 A:ASP739 2.2 23.8 1.0
OD1 A:ASP747 2.3 25.8 1.0
O A:LEU745 2.3 20.9 1.0
OD1 A:ASP743 2.3 25.2 1.0
OD1 A:ASN741 2.3 26.5 1.0
O A:HOH1330 2.4 27.2 1.0
CG A:ASP743 3.3 27.2 1.0
CG A:ASN741 3.4 30.3 1.0
CG A:ASP739 3.4 22.9 1.0
C A:LEU745 3.5 22.8 1.0
CG A:ASP747 3.5 25.1 1.0
OD2 A:ASP743 3.7 29.7 1.0
ND2 A:ASN741 3.9 30.7 1.0
CA A:ASP739 4.0 21.4 1.0
N A:ASP747 4.0 21.4 1.0
N A:LEU745 4.1 21.8 1.0
C A:ARG746 4.1 23.4 1.0
CB A:ASP739 4.2 23.4 1.0
CA A:LEU745 4.2 21.7 1.0
CA A:ASP747 4.2 23.2 1.0
O A:ARG746 4.3 22.3 1.0
OD2 A:ASP739 4.3 22.9 1.0
N A:ASP743 4.3 24.6 1.0
OD2 A:ASP747 4.4 25.8 1.0
CB A:LEU745 4.4 25.7 1.0
N A:ASN741 4.5 24.4 1.0
C A:ASP739 4.5 23.4 1.0
O A:PHE738 4.5 20.5 1.0
CB A:ASP743 4.5 27.3 1.0
N A:ARG746 4.5 23.3 1.0
CB A:ASP747 4.5 22.7 1.0
OE2 A:GLU751 4.7 43.1 1.0
CB A:ASN741 4.7 27.9 1.0
CA A:ARG746 4.7 22.8 1.0
N A:TYR740 4.7 22.5 1.0
N A:TYR742 4.8 23.4 1.0
CA A:ASP743 4.8 24.1 1.0
O A:HOH1310 4.8 42.1 1.0
C A:ASN741 4.8 26.8 1.0
N A:GLY744 4.9 24.4 1.0
CA A:ASN741 4.9 27.2 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 15:36:58 2025

Last articles

Mo in 9CU2
Mo in 9CU1
Mo in 8RHP
Mo in 9CU0
Mo in 9CTZ
Mo in 9CJD
Mo in 9CJF
Mo in 9CJC
Mo in 9CJE
Mo in 9CJB
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy