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Calcium in PDB 7g3h: Crystal Structure of Rat Autotaxin in Complex with [2-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CLC1CCC2C(C1) C[C@@H](C2)NC1NCC(CN1)C(=O)N1CCC21COC2 with IC50=0.0678127 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [2-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CLC1CCC2C(C1) C[C@@H](C2)NC1NCC(CN1)C(=O)N1CCC21COC2 with IC50=0.0678127 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [2-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CLC1CCC2C(C1) C[C@@H](C2)NC1NCC(CN1)C(=O)N1CCC21COC2 with IC50=0.0678127 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [2-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CLC1CCC2C(C1) C[C@@H](C2)NC1NCC(CN1)C(=O)N1CCC21COC2 with IC50=0.0678127 Microm, PDB code: 7g3h 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) 72.40 / 1.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.504, 91.217, 119.043, 90, 90, 90
R / Rfree (%) 16.9 / 19.8

Other elements in 7g3h:

The structure of Crystal Structure of Rat Autotaxin in Complex with [2-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CLC1CCC2C(C1) C[C@@H](C2)NC1NCC(CN1)C(=O)N1CCC21COC2 with IC50=0.0678127 Microm also contains other interesting chemical elements:

Potassium (K) 1 atom
Chlorine (Cl) 3 atoms
Zinc (Zn) 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-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CLC1CCC2C(C1) C[C@@H](C2)NC1NCC(CN1)C(=O)N1CCC21COC2 with IC50=0.0678127 Microm (pdb code 7g3h). 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-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CLC1CCC2C(C1) C[C@@H](C2)NC1NCC(CN1)C(=O)N1CCC21COC2 with IC50=0.0678127 Microm, PDB code: 7g3h:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g3h

Go back to Calcium Binding Sites List in 7g3h
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [2-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CLC1CCC2C(C1) C[C@@H](C2)NC1NCC(CN1)C(=O)N1CCC21COC2 with IC50=0.0678127 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-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CLC1CCC2C(C1) C[C@@H](C2)NC1NCC(CN1)C(=O)N1CCC21COC2 with IC50=0.0678127 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:16.7
occ:1.00
 OD1 A:ASP739 2.3 16.8 1.0
OD1 A:ASN741 2.3 19.4 1.0
OD1 A:ASP747 2.3 18.7 1.0
O A:LEU745 2.3 15.5 1.0
O A:HOH1439 2.3 20.2 1.0
OD1 A:ASP743 2.4 20.6 1.0
CG A:ASP743 3.3 20.7 1.0
CG A:ASN741 3.3 23.9 1.0
CG A:ASP739 3.4 17.2 1.0
C A:LEU745 3.5 16.3 1.0
CG A:ASP747 3.5 19.4 1.0
OD2 A:ASP743 3.7 21.5 1.0
ND2 A:ASN741 3.8 26.0 1.0
N A:ASP747 3.9 15.9 1.0
CA A:ASP739 4.0 15.7 1.0
C A:ARG746 4.1 17.4 1.0
N A:LEU745 4.1 14.6 1.0
CA A:ASP747 4.2 17.3 1.0
CB A:ASP739 4.2 16.5 1.0
CA A:LEU745 4.2 15.9 1.0
O A:ARG746 4.2 16.5 1.0
N A:ASP743 4.3 17.8 1.0
OD2 A:ASP739 4.4 16.5 1.0
OD2 A:ASP747 4.4 20.6 1.0
N A:ASN741 4.5 17.1 1.0
CB A:LEU745 4.5 17.7 1.0
CB A:ASP747 4.5 17.7 1.0
O A:PHE738 4.5 16.2 1.0
N A:ARG746 4.5 15.8 1.0
C A:ASP739 4.5 16.5 1.0
CB A:ASP743 4.5 19.2 1.0
CB A:ASN741 4.6 20.7 1.0
O A:HOH1414 4.6 41.8 1.0
CA A:ARG746 4.7 16.4 1.0
N A:TYR740 4.8 16.8 1.0
N A:TYR742 4.8 19.5 1.0
OE2 A:GLU751 4.8 35.3 1.0
CA A:ASN741 4.8 19.5 1.0
C A:ASN741 4.8 20.5 1.0
CA A:ASP743 4.9 17.7 1.0
N A:GLY744 4.9 17.7 1.0

Calcium binding site 2 out of 2 in 7g3h

Go back to Calcium Binding Sites List in 7g3h
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [2-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CLC1CCC2C(C1) C[C@@H](C2)NC1NCC(CN1)C(=O)N1CCC21COC2 with IC50=0.0678127 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-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CLC1CCC2C(C1) C[C@@H](C2)NC1NCC(CN1)C(=O)N1CCC21COC2 with IC50=0.0678127 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:24.9
occ:1.00
 OD1 A:ASP171 1.8 24.6 1.0
OG1 A:THR209 1.9 19.2 1.0
NE2 A:HIS359 2.1 18.3 1.0
OD2 A:ASP358 2.2 21.1 1.0
CG A:ASP171 2.7 24.3 1.0
CB A:THR209 3.0 20.0 1.0
OD2 A:ASP171 3.0 33.0 1.0
CE1 A:HIS359 3.0 18.0 1.0
CD2 A:HIS359 3.0 17.4 1.0
CG A:ASP358 3.1 19.3 1.0
CG2 A:THR209 3.2 22.4 1.0
OD1 A:ASP358 3.3 16.9 1.0
CA A:THR209 3.4 17.4 1.0
O A:HOH1017 3.5 36.5 1.0
CB A:ASP171 4.0 20.2 1.0
N A:THR209 4.0 16.7 1.0
ND1 A:HIS359 4.0 16.7 1.0
OD1 A:ASP311 4.1 21.9 1.0
CG A:HIS359 4.1 16.0 1.0
N A:GLY172 4.2 17.9 1.0
O A:ACT908 4.2 32.8 1.0
CA A:ASP171 4.3 19.0 1.0
CG A:ASP311 4.3 20.4 1.0
CE1 A:HIS474 4.3 17.1 1.0
CB A:ASP358 4.4 17.4 1.0
O A:HOH1001 4.5 25.7 1.0
ZN A:ZN901 4.5 20.4 1.0
NE2 A:HIS474 4.5 17.4 1.0
C A:ASP171 4.6 18.6 1.0
CB A:ASP311 4.7 18.8 1.0
C A:THR209 4.7 17.9 1.0
C A:LYS208 4.8 17.4 1.0
OD2 A:ASP311 4.8 25.3 1.0
OH A:TYR306 4.9 31.2 1.0
CA A:GLY172 5.0 17.7 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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