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Calcium in PDB 7g3w: Crystal Structure of Rat Autotaxin in Complex with N-[(2R)-5-Chloro-2, 3-Dihydro-1H-Inden-2-Yl]-5-(3-Methyl-1,2,4-Oxadiazol-5-Yl)Pyrimidin- 2-Amine, I.E. Smiles C1C(Cnc(N1)N[C@H]1CC2CC(Cl)CCC2C1)C1=Nc(=NO1)C with IC50=0.186827 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with N-[(2R)-5-Chloro-2, 3-Dihydro-1H-Inden-2-Yl]-5-(3-Methyl-1,2,4-Oxadiazol-5-Yl)Pyrimidin- 2-Amine, I.E. Smiles C1C(Cnc(N1)N[C@H]1CC2CC(Cl)CCC2C1)C1=Nc(=NO1)C with IC50=0.186827 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with N-[(2R)-5-Chloro-2, 3-Dihydro-1H-Inden-2-Yl]-5-(3-Methyl-1,2,4-Oxadiazol-5-Yl)Pyrimidin- 2-Amine, I.E. Smiles C1C(Cnc(N1)N[C@H]1CC2CC(Cl)CCC2C1)C1=Nc(=NO1)C with IC50=0.186827 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with N-[(2R)-5-Chloro-2, 3-Dihydro-1H-Inden-2-Yl]-5-(3-Methyl-1,2,4-Oxadiazol-5-Yl)Pyrimidin- 2-Amine, I.E. Smiles C1C(Cnc(N1)N[C@H]1CC2CC(Cl)CCC2C1)C1=Nc(=NO1)C with IC50=0.186827 Microm, PDB code: 7g3w 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) 72.89 / 1.51
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.916, 91.923, 119.613, 90, 90, 90
R / Rfree (%) 17.1 / 20.7

Other elements in 7g3w:

The structure of Crystal Structure of Rat Autotaxin in Complex with N-[(2R)-5-Chloro-2, 3-Dihydro-1H-Inden-2-Yl]-5-(3-Methyl-1,2,4-Oxadiazol-5-Yl)Pyrimidin- 2-Amine, I.E. Smiles C1C(Cnc(N1)N[C@H]1CC2CC(Cl)CCC2C1)C1=Nc(=NO1)C with IC50=0.186827 Microm also contains other interesting chemical elements:

Sodium (Na) 1 atom
Chlorine (Cl) 1 atom
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 N-[(2R)-5-Chloro-2, 3-Dihydro-1H-Inden-2-Yl]-5-(3-Methyl-1,2,4-Oxadiazol-5-Yl)Pyrimidin- 2-Amine, I.E. Smiles C1C(Cnc(N1)N[C@H]1CC2CC(Cl)CCC2C1)C1=Nc(=NO1)C with IC50=0.186827 Microm (pdb code 7g3w). 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 N-[(2R)-5-Chloro-2, 3-Dihydro-1H-Inden-2-Yl]-5-(3-Methyl-1,2,4-Oxadiazol-5-Yl)Pyrimidin- 2-Amine, I.E. Smiles C1C(Cnc(N1)N[C@H]1CC2CC(Cl)CCC2C1)C1=Nc(=NO1)C with IC50=0.186827 Microm, PDB code: 7g3w:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g3w

Go back to Calcium Binding Sites List in 7g3w
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with N-[(2R)-5-Chloro-2, 3-Dihydro-1H-Inden-2-Yl]-5-(3-Methyl-1,2,4-Oxadiazol-5-Yl)Pyrimidin- 2-Amine, I.E. Smiles C1C(Cnc(N1)N[C@H]1CC2CC(Cl)CCC2C1)C1=Nc(=NO1)C with IC50=0.186827 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 N-[(2R)-5-Chloro-2, 3-Dihydro-1H-Inden-2-Yl]-5-(3-Methyl-1,2,4-Oxadiazol-5-Yl)Pyrimidin- 2-Amine, I.E. Smiles C1C(Cnc(N1)N[C@H]1CC2CC(Cl)CCC2C1)C1=Nc(=NO1)C with IC50=0.186827 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:21.4
occ:1.00
 OD1 A:ASP171 1.8 20.9 0.5
OG1 A:THR209 1.8 17.2 1.0
OD1 A:ASP171 1.9 18.0 0.5
NE2 A:HIS359 2.0 13.2 1.0
OD2 A:ASP358 2.3 18.7 1.0
CG A:ASP171 2.6 14.8 0.5
OD2 A:ASP171 2.7 18.1 0.5
CG A:ASP171 2.8 18.9 0.5
CB A:THR209 2.9 17.2 1.0
CE1 A:HIS359 2.9 14.1 1.0
CD2 A:HIS359 3.0 13.4 1.0
CG A:ASP358 3.1 16.3 1.0
CG2 A:THR209 3.2 19.8 1.0
OD2 A:ASP171 3.3 19.7 0.5
CA A:THR209 3.3 13.6 1.0
OD1 A:ASP358 3.4 13.7 1.0
O A:HOH1140 3.5 28.9 1.0
N A:THR209 3.9 14.6 1.0
CB A:ASP171 3.9 14.2 0.5
CB A:ASP171 4.0 16.2 0.5
ND1 A:HIS359 4.0 14.8 1.0
OD1 A:ASP311 4.0 19.9 1.0
CG A:HIS359 4.1 12.5 1.0
N A:GLY172 4.2 12.6 1.0
CA A:ASP171 4.3 15.7 0.5
CA A:ASP171 4.3 14.8 0.5
CE1 A:HIS474 4.4 16.0 1.0
CB A:ASP358 4.4 13.9 1.0
CG A:ASP311 4.4 15.4 1.0
O A:HOH1001 4.4 21.1 1.0
O A:HOH1572 4.5 29.8 1.0
ZN A:ZN906 4.5 15.8 1.0
NE2 A:HIS474 4.5 14.8 1.0
C A:ASP171 4.6 14.7 1.0
C A:THR209 4.7 13.9 1.0
C A:LYS208 4.7 13.2 1.0
CB A:ASP311 4.8 14.3 1.0
OD2 A:ASP311 4.9 22.2 1.0
OH A:TYR306 4.9 23.1 1.0

Calcium binding site 2 out of 2 in 7g3w

Go back to Calcium Binding Sites List in 7g3w
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with N-[(2R)-5-Chloro-2, 3-Dihydro-1H-Inden-2-Yl]-5-(3-Methyl-1,2,4-Oxadiazol-5-Yl)Pyrimidin- 2-Amine, I.E. Smiles C1C(Cnc(N1)N[C@H]1CC2CC(Cl)CCC2C1)C1=Nc(=NO1)C with IC50=0.186827 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 N-[(2R)-5-Chloro-2, 3-Dihydro-1H-Inden-2-Yl]-5-(3-Methyl-1,2,4-Oxadiazol-5-Yl)Pyrimidin- 2-Amine, I.E. Smiles C1C(Cnc(N1)N[C@H]1CC2CC(Cl)CCC2C1)C1=Nc(=NO1)C with IC50=0.186827 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:13.1
occ:1.00
 OD1 A:ASP747 2.3 14.0 1.0
O A:HOH1462 2.3 18.1 1.0
OD1 A:ASP739 2.3 13.7 1.0
OD1 A:ASN741 2.3 15.6 1.0
O A:LEU745 2.3 12.7 1.0
OD1 A:ASP743 2.4 14.5 1.0
CG A:ASP743 3.3 17.2 1.0
CG A:ASN741 3.4 16.0 1.0
CG A:ASP739 3.4 12.7 1.0
C A:LEU745 3.5 11.5 1.0
CG A:ASP747 3.5 12.9 1.0
OD2 A:ASP743 3.7 19.4 1.0
ND2 A:ASN741 3.9 20.2 1.0
CA A:ASP739 3.9 11.7 1.0
N A:ASP747 4.0 12.3 1.0
C A:ARG746 4.0 14.4 1.0
N A:LEU745 4.1 12.4 1.0
CA A:ASP747 4.1 12.7 1.0
CB A:ASP739 4.1 12.5 1.0
CA A:LEU745 4.2 12.6 1.0
O A:ARG746 4.2 14.8 1.0
N A:ASP743 4.3 15.8 1.0
CB A:ASP747 4.4 12.8 1.0
CB A:LEU745 4.4 13.7 1.0
OD2 A:ASP747 4.4 13.2 1.0
OD2 A:ASP739 4.4 13.1 1.0
O A:PHE738 4.5 12.9 1.0
C A:ASP739 4.5 13.5 1.0
N A:ASN741 4.5 13.8 1.0
CB A:ASP743 4.5 15.3 1.0
N A:ARG746 4.5 12.4 1.0
OE2 A:GLU751 4.5 23.7 1.0
CB A:ASN741 4.7 15.8 1.0
O A:HOH1486 4.7 26.2 1.0
CA A:ARG746 4.8 13.4 1.0
N A:TYR740 4.8 14.9 1.0
N A:TYR742 4.8 13.6 1.0
CA A:ASP743 4.8 13.6 1.0
C A:ASN741 4.9 14.7 1.0
CA A:ASN741 4.9 13.6 1.0
N A:GLY744 4.9 12.3 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 22:23:20 2025

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