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Calcium in PDB 7g3v: Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[[5-(6-Methoxypyrimidin-4-Yl)-1-Methylimidazol-2- Yl]Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C(N1C)C1CC(NCN1)Oc)Cl)C#N with IC50=0.0417382 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[[5-(6-Methoxypyrimidin-4-Yl)-1-Methylimidazol-2- Yl]Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C(N1C)C1CC(NCN1)Oc)Cl)C#N with IC50=0.0417382 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[[5-(6-Methoxypyrimidin-4-Yl)-1-Methylimidazol-2- Yl]Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C(N1C)C1CC(NCN1)Oc)Cl)C#N with IC50=0.0417382 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-[[5-(6-Methoxypyrimidin-4-Yl)-1-Methylimidazol-2- Yl]Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C(N1C)C1CC(NCN1)Oc)Cl)C#N with IC50=0.0417382 Microm, PDB code: 7g3v 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) 73.25 / 1.74
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.309, 92.075, 120.892, 90, 90, 90
R / Rfree (%) 19.4 / 24.3

Other elements in 7g3v:

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[[5-(6-Methoxypyrimidin-4-Yl)-1-Methylimidazol-2- Yl]Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C(N1C)C1CC(NCN1)Oc)Cl)C#N with IC50=0.0417382 Microm also contains other interesting chemical elements:

Sodium (Na) 1 atom
Potassium (K) 1 atom
Zinc (Zn) 1 atom
Chlorine (Cl) 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-[[5-(6-Methoxypyrimidin-4-Yl)-1-Methylimidazol-2- Yl]Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C(N1C)C1CC(NCN1)Oc)Cl)C#N with IC50=0.0417382 Microm (pdb code 7g3v). 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-[[5-(6-Methoxypyrimidin-4-Yl)-1-Methylimidazol-2- Yl]Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C(N1C)C1CC(NCN1)Oc)Cl)C#N with IC50=0.0417382 Microm, PDB code: 7g3v:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g3v

Go back to Calcium Binding Sites List in 7g3v
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[[5-(6-Methoxypyrimidin-4-Yl)-1-Methylimidazol-2- Yl]Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C(N1C)C1CC(NCN1)Oc)Cl)C#N with IC50=0.0417382 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-[[5-(6-Methoxypyrimidin-4-Yl)-1-Methylimidazol-2- Yl]Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C(N1C)C1CC(NCN1)Oc)Cl)C#N with IC50=0.0417382 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:13.1
occ:1.00
 OD1 A:ASP739 2.2 11.8 1.0
OD1 A:ASP747 2.3 16.6 1.0
OD1 A:ASP743 2.3 15.6 1.0
O A:LEU745 2.3 13.9 1.0
O A:HOH1320 2.3 16.5 1.0
OD1 A:ASN741 2.4 16.9 1.0
CG A:ASP743 3.3 15.7 1.0
CG A:ASP739 3.4 13.1 1.0
CG A:ASN741 3.5 18.7 1.0
C A:LEU745 3.5 12.8 1.0
CG A:ASP747 3.5 14.9 1.0
OD2 A:ASP743 3.8 18.0 1.0
ND2 A:ASN741 3.9 19.2 1.0
CA A:ASP739 3.9 12.1 1.0
N A:ASP747 4.0 12.3 1.0
C A:ARG746 4.1 13.4 1.0
N A:LEU745 4.1 12.4 1.0
CA A:ASP747 4.2 14.4 1.0
CB A:ASP739 4.2 13.2 1.0
N A:ASP743 4.3 14.8 1.0
O A:ARG746 4.3 12.1 1.0
CA A:LEU745 4.3 12.6 1.0
OD2 A:ASP747 4.4 15.0 1.0
OD2 A:ASP739 4.4 12.3 1.0
O A:PHE738 4.4 11.7 1.0
CB A:ASP747 4.4 13.5 1.0
CB A:ASP743 4.5 14.8 1.0
C A:ASP739 4.5 13.8 1.0
N A:ASN741 4.5 16.3 1.0
CB A:LEU745 4.5 14.4 1.0
N A:ARG746 4.5 13.2 1.0
OE2 A:GLU751 4.6 25.4 1.0
O A:HOH1209 4.6 29.1 1.0
N A:TYR740 4.7 15.1 1.0
CB A:ASN741 4.8 17.6 1.0
N A:TYR742 4.8 16.7 1.0
CA A:ASP743 4.8 14.6 1.0
CA A:ARG746 4.8 13.7 1.0
N A:GLY744 4.9 12.6 1.0
C A:ASN741 4.9 18.0 1.0
CA A:ASN741 5.0 18.5 1.0

Calcium binding site 2 out of 2 in 7g3v

Go back to Calcium Binding Sites List in 7g3v
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[[5-(6-Methoxypyrimidin-4-Yl)-1-Methylimidazol-2- Yl]Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C(N1C)C1CC(NCN1)Oc)Cl)C#N with IC50=0.0417382 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-[[5-(6-Methoxypyrimidin-4-Yl)-1-Methylimidazol-2- Yl]Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C(N1C)C1CC(NCN1)Oc)Cl)C#N with IC50=0.0417382 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:39.3
occ:1.00
 OD1 A:ASP171 1.9 23.5 1.0
OG1 A:THR209 2.0 23.4 1.0
NE2 A:HIS359 2.2 13.8 1.0
OD2 A:ASP358 2.5 20.7 1.0
CG A:ASP171 2.5 19.6 1.0
OD2 A:ASP171 2.6 27.5 1.0
CB A:THR209 3.0 18.8 1.0
CE1 A:HIS359 3.0 13.1 1.0
O A:HOH1044 3.2 29.3 1.0
CD2 A:HIS359 3.2 14.2 1.0
CG A:ASP358 3.2 16.5 1.0
CG2 A:THR209 3.3 22.8 1.0
CA A:THR209 3.4 15.8 1.0
OD1 A:ASP358 3.4 12.9 1.0
O2 A:SO4909 3.5 51.6 1.0
N A:THR209 3.8 15.4 1.0
CB A:ASP171 3.9 17.6 1.0
OD1 A:ASP311 4.1 16.7 1.0
ND1 A:HIS359 4.2 13.1 1.0
O A:HOH1001 4.2 22.8 1.0
CG A:HIS359 4.2 13.5 1.0
CA A:ASP171 4.2 15.3 1.0
N A:GLY172 4.3 14.3 1.0
CG A:ASP311 4.3 14.2 1.0
CE1 A:HIS474 4.4 17.3 1.0
ZN A:ZN902 4.5 18.6 1.0
NE2 A:HIS474 4.5 15.6 1.0
CB A:ASP358 4.6 14.5 1.0
O1 A:SO4909 4.6 89.4 1.0
C A:ASP171 4.6 14.5 1.0
OD2 A:ASP311 4.7 19.1 1.0
C A:LYS208 4.7 14.9 1.0
C A:THR209 4.7 14.8 1.0
S A:SO4909 4.7 71.5 1.0
CB A:ASP311 4.8 15.7 1.0
OH A:TYR306 4.9 25.1 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 15:43:01 2025

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