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Calcium in PDB 7g3i: Crystal Structure of Rat Autotaxin in Complex with (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm, PDB code: 7g3i 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) 61.81 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.988, 91.306, 118.107, 90, 90, 90
R / Rfree (%) 17.2 / 21.2

Other elements in 7g3i:

The structure of Crystal Structure of Rat Autotaxin in Complex with (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm (pdb code 7g3i). 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 (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm, PDB code: 7g3i:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g3i

Go back to Calcium Binding Sites List in 7g3i
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 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 (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:16.1
occ:1.00
 OD1 A:ASP747 2.2 17.5 1.0
OD1 A:ASN741 2.3 18.9 1.0
OD1 A:ASP739 2.3 16.1 1.0
O A:HOH1376 2.3 19.8 1.0
O A:LEU745 2.3 14.9 1.0
OD1 A:ASP743 2.4 18.8 1.0
CG A:ASP743 3.3 19.3 1.0
CG A:ASN741 3.3 20.4 1.0
CG A:ASP739 3.4 16.9 1.0
CG A:ASP747 3.5 17.6 1.0
C A:LEU745 3.5 16.2 1.0
OD2 A:ASP743 3.6 20.2 1.0
ND2 A:ASN741 3.7 24.3 1.0
N A:ASP747 3.9 16.2 1.0
CA A:ASP739 4.0 16.3 1.0
N A:LEU745 4.1 17.6 1.0
C A:ARG746 4.1 17.0 1.0
CA A:ASP747 4.2 16.9 1.0
CB A:ASP739 4.2 16.3 1.0
CA A:LEU745 4.2 16.7 1.0
O A:ARG746 4.3 15.6 1.0
OD2 A:ASP747 4.3 18.2 1.0
N A:ASP743 4.3 17.6 1.0
OD2 A:ASP739 4.3 15.5 1.0
CB A:LEU745 4.5 18.7 1.0
CB A:ASP747 4.5 17.0 1.0
N A:ASN741 4.5 18.0 1.0
C A:ASP739 4.5 17.8 1.0
CB A:ASP743 4.5 17.8 1.0
O A:PHE738 4.5 16.5 1.0
N A:ARG746 4.5 16.1 1.0
CB A:ASN741 4.6 20.0 1.0
N A:TYR740 4.7 17.1 1.0
N A:TYR742 4.7 18.2 1.0
CA A:ASP743 4.8 18.2 1.0
CA A:ARG746 4.8 18.1 1.0
OE2 A:GLU751 4.8 36.1 1.0
N A:GLY744 4.8 18.5 1.0
C A:ASN741 4.8 19.5 1.0
CA A:ASN741 4.9 18.6 1.0

Calcium binding site 2 out of 2 in 7g3i

Go back to Calcium Binding Sites List in 7g3i
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 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 (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:14.8
occ:1.00
 OD1 A:ASP171 1.9 19.8 1.0
OG1 A:THR209 2.0 17.6 1.0
NE2 A:HIS359 2.2 18.1 1.0
OD2 A:ASP358 2.2 21.0 1.0
O A:ACT909 2.3 31.7 1.0
CG A:ASP171 2.7 20.0 1.0
OD2 A:ASP171 2.8 24.2 1.0
CE1 A:HIS359 3.1 18.3 1.0
CB A:THR209 3.1 19.2 1.0
CD2 A:HIS359 3.1 17.1 1.0
CG A:ASP358 3.1 21.7 1.0
C A:ACT909 3.3 36.2 1.0
CG2 A:THR209 3.4 19.8 1.0
OD1 A:ASP358 3.5 18.3 1.0
CA A:THR209 3.6 18.1 1.0
CH3 A:ACT909 3.8 36.0 1.0
OD1 A:ASP311 4.0 20.7 1.0
CB A:ASP171 4.1 19.2 1.0
N A:THR209 4.1 17.5 1.0
ND1 A:HIS359 4.2 16.4 1.0
CG A:HIS359 4.2 16.9 1.0
N A:GLY172 4.3 18.7 1.0
CE1 A:HIS474 4.3 16.3 1.0
CG A:ASP311 4.3 20.4 1.0
O A:HOH1167 4.4 9.6 0.5
OXT A:ACT909 4.4 30.6 1.0
ZN A:ZN902 4.4 20.6 1.0
CA A:ASP171 4.4 18.2 1.0
CB A:ASP358 4.5 18.6 1.0
NE2 A:HIS474 4.5 16.4 1.0
C A:ASP171 4.7 19.5 1.0
CB A:ASP311 4.7 19.1 1.0
OD2 A:ASP311 4.9 23.1 1.0
C A:LYS208 4.9 19.0 1.0
C A:THR209 4.9 17.0 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: Sat Feb 8 15:38:37 2025

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