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Calcium in PDB 7g3p: Crystal Structure of Rat Autotaxin in Complex with [2-[(4,6-Dichloro- 2,3-Dihydro-1H-Inden-2-Yl)Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles C1(Cl) C2C[C@@H](NC3NCC(CN3)C(=O)N3CCC43COC4)CC2CC(Cl)C1 with IC50=0.0133598 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [2-[(4,6-Dichloro- 2,3-Dihydro-1H-Inden-2-Yl)Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles C1(Cl) C2C[C@@H](NC3NCC(CN3)C(=O)N3CCC43COC4)CC2CC(Cl)C1 with IC50=0.0133598 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [2-[(4,6-Dichloro- 2,3-Dihydro-1H-Inden-2-Yl)Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles C1(Cl) C2C[C@@H](NC3NCC(CN3)C(=O)N3CCC43COC4)CC2CC(Cl)C1 with IC50=0.0133598 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [2-[(4,6-Dichloro- 2,3-Dihydro-1H-Inden-2-Yl)Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles C1(Cl) C2C[C@@H](NC3NCC(CN3)C(=O)N3CCC43COC4)CC2CC(Cl)C1 with IC50=0.0133598 Microm, PDB code: 7g3p 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) 68.81 / 1.58
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.842, 91.574, 119.916, 90, 90, 90
R / Rfree (%) 16.9 / 19.9

Other elements in 7g3p:

The structure of Crystal Structure of Rat Autotaxin in Complex with [2-[(4,6-Dichloro- 2,3-Dihydro-1H-Inden-2-Yl)Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles C1(Cl) C2C[C@@H](NC3NCC(CN3)C(=O)N3CCC43COC4)CC2CC(Cl)C1 with IC50=0.0133598 Microm also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
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 [2-[(4,6-Dichloro- 2,3-Dihydro-1H-Inden-2-Yl)Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles C1(Cl) C2C[C@@H](NC3NCC(CN3)C(=O)N3CCC43COC4)CC2CC(Cl)C1 with IC50=0.0133598 Microm (pdb code 7g3p). 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 [2-[(4,6-Dichloro- 2,3-Dihydro-1H-Inden-2-Yl)Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles C1(Cl) C2C[C@@H](NC3NCC(CN3)C(=O)N3CCC43COC4)CC2CC(Cl)C1 with IC50=0.0133598 Microm, PDB code: 7g3p:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g3p

Go back to Calcium Binding Sites List in 7g3p
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [2-[(4,6-Dichloro- 2,3-Dihydro-1H-Inden-2-Yl)Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles C1(Cl) C2C[C@@H](NC3NCC(CN3)C(=O)N3CCC43COC4)CC2CC(Cl)C1 with IC50=0.0133598 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 [2-[(4,6-Dichloro- 2,3-Dihydro-1H-Inden-2-Yl)Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles C1(Cl) C2C[C@@H](NC3NCC(CN3)C(=O)N3CCC43COC4)CC2CC(Cl)C1 with IC50=0.0133598 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:38.9
occ:1.00
 OD1 A:ASP171 1.8 21.9 1.0
OG1 A:THR209 1.8 18.9 1.0
NE2 A:HIS359 2.1 15.0 1.0
OD2 A:ASP358 2.4 17.4 1.0
CG A:ASP171 2.8 21.0 1.0
CB A:THR209 2.8 18.0 1.0
CE1 A:HIS359 2.9 15.1 1.0
CG2 A:THR209 3.0 20.1 1.0
CD2 A:HIS359 3.2 14.9 1.0
OD2 A:ASP171 3.2 28.4 1.0
CG A:ASP358 3.2 16.8 1.0
O A:HOH1171 3.3 24.8 1.0
CA A:THR209 3.3 15.0 1.0
OD1 A:ASP358 3.5 14.2 1.0
N A:THR209 3.9 14.8 1.0
OD1 A:ASP311 4.0 21.3 1.0
CB A:ASP171 4.0 16.9 1.0
ND1 A:HIS359 4.1 15.0 1.0
CG A:HIS359 4.2 13.5 1.0
CE1 A:HIS474 4.3 15.8 1.0
CG A:ASP311 4.3 18.1 1.0
N A:GLY172 4.3 14.8 1.0
CA A:ASP171 4.4 16.3 1.0
NE2 A:HIS474 4.4 13.4 1.0
ZN A:ZN902 4.4 17.7 1.0
O A:HOH1500 4.4 24.4 1.0
CB A:ASP358 4.5 15.6 1.0
O A:HOH1003 4.6 9.2 0.5
C A:THR209 4.6 15.7 1.0
C A:ASP171 4.7 15.0 1.0
C A:LYS208 4.7 15.6 1.0
OD2 A:ASP311 4.8 22.6 1.0
OH A:TYR306 4.8 23.4 1.0
CB A:ASP311 4.8 17.8 1.0

Calcium binding site 2 out of 2 in 7g3p

Go back to Calcium Binding Sites List in 7g3p
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [2-[(4,6-Dichloro- 2,3-Dihydro-1H-Inden-2-Yl)Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles C1(Cl) C2C[C@@H](NC3NCC(CN3)C(=O)N3CCC43COC4)CC2CC(Cl)C1 with IC50=0.0133598 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 [2-[(4,6-Dichloro- 2,3-Dihydro-1H-Inden-2-Yl)Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles C1(Cl) C2C[C@@H](NC3NCC(CN3)C(=O)N3CCC43COC4)CC2CC(Cl)C1 with IC50=0.0133598 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:14.0
occ:1.00
 OD1 A:ASP747 2.2 15.1 1.0
O A:HOH1434 2.3 18.2 1.0
OD1 A:ASP739 2.3 13.8 1.0
OD1 A:ASN741 2.3 18.3 1.0
O A:LEU745 2.3 15.3 1.0
OD1 A:ASP743 2.4 15.3 1.0
CG A:ASP743 3.3 18.6 1.0
CG A:ASN741 3.4 18.6 1.0
CG A:ASP739 3.4 14.8 1.0
C A:LEU745 3.5 13.8 1.0
CG A:ASP747 3.5 13.5 1.0
OD2 A:ASP743 3.8 19.1 1.0
ND2 A:ASN741 3.9 20.4 1.0
CA A:ASP739 3.9 12.6 1.0
N A:ASP747 4.0 13.6 1.0
C A:ARG746 4.0 14.3 1.0
N A:LEU745 4.1 12.9 1.0
CB A:ASP739 4.1 13.7 1.0
CA A:ASP747 4.2 13.2 1.0
CA A:LEU745 4.2 13.5 1.0
O A:ARG746 4.2 13.8 1.0
N A:ASP743 4.3 14.6 1.0
OD2 A:ASP739 4.4 14.7 1.0
OD2 A:ASP747 4.4 15.4 1.0
CB A:ASP747 4.4 12.6 1.0
N A:ASN741 4.4 16.2 1.0
O A:PHE738 4.4 11.7 1.0
CB A:LEU745 4.5 14.2 1.0
N A:ARG746 4.5 14.1 1.0
C A:ASP739 4.5 14.3 1.0
CB A:ASP743 4.5 16.5 1.0
OE2 A:GLU751 4.5 30.1 1.0
CB A:ASN741 4.7 16.9 1.0
N A:TYR740 4.7 15.2 1.0
O A:HOH1431 4.7 28.7 1.0
CA A:ARG746 4.7 14.5 1.0
N A:TYR742 4.8 15.7 1.0
CA A:ASP743 4.8 14.9 1.0
CA A:ASN741 4.9 16.4 1.0
C A:ASN741 4.9 16.7 1.0
N A:GLY744 4.9 14.3 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: Sat Feb 8 15:38:32 2025

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