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Calcium in PDB 7g3n: Crystal Structure of Rat Autotaxin in Complex with [2-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Hydroxy-6-Methyl- 1-Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CC1(O) CC2(CCN2C(=O)C3CNC(N[C@@H]4CC5CCC(Cl)CC5C4)NC3)C1 with IC50=0.0155951 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-Hydroxy-6-Methyl- 1-Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CC1(O) CC2(CCN2C(=O)C3CNC(N[C@@H]4CC5CCC(Cl)CC5C4)NC3)C1 with IC50=0.0155951 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-Hydroxy-6-Methyl- 1-Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CC1(O) CC2(CCN2C(=O)C3CNC(N[C@@H]4CC5CCC(Cl)CC5C4)NC3)C1 with IC50=0.0155951 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-Hydroxy-6-Methyl- 1-Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CC1(O) CC2(CCN2C(=O)C3CNC(N[C@@H]4CC5CCC(Cl)CC5C4)NC3)C1 with IC50=0.0155951 Microm, PDB code: 7g3n 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) 72.33 / 1.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.547, 91.147, 118.846, 90, 90, 90
R / Rfree (%) 16.3 / 20

Other elements in 7g3n:

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-Hydroxy-6-Methyl- 1-Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CC1(O) CC2(CCN2C(=O)C3CNC(N[C@@H]4CC5CCC(Cl)CC5C4)NC3)C1 with IC50=0.0155951 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 [2-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Hydroxy-6-Methyl- 1-Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CC1(O) CC2(CCN2C(=O)C3CNC(N[C@@H]4CC5CCC(Cl)CC5C4)NC3)C1 with IC50=0.0155951 Microm (pdb code 7g3n). 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-Hydroxy-6-Methyl- 1-Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CC1(O) CC2(CCN2C(=O)C3CNC(N[C@@H]4CC5CCC(Cl)CC5C4)NC3)C1 with IC50=0.0155951 Microm, PDB code: 7g3n:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g3n

Go back to Calcium Binding Sites List in 7g3n
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-Hydroxy-6-Methyl- 1-Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CC1(O) CC2(CCN2C(=O)C3CNC(N[C@@H]4CC5CCC(Cl)CC5C4)NC3)C1 with IC50=0.0155951 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-Hydroxy-6-Methyl- 1-Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CC1(O) CC2(CCN2C(=O)C3CNC(N[C@@H]4CC5CCC(Cl)CC5C4)NC3)C1 with IC50=0.0155951 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:20.4
occ:1.00
 OD1 A:ASP171 1.9 23.2 1.0
OG1 A:THR209 1.9 20.8 1.0
NE2 A:HIS359 2.1 18.7 1.0
OD2 A:ASP358 2.2 22.2 1.0
O A:ACT908 2.6 46.4 1.0
CG A:ASP171 2.7 23.2 1.0
OD2 A:ASP171 2.8 29.6 1.0
CB A:THR209 3.0 20.8 1.0
CG A:ASP358 3.0 20.6 1.0
CD2 A:HIS359 3.0 17.5 1.0
CE1 A:HIS359 3.0 18.7 1.0
OD1 A:ASP358 3.2 17.7 1.0
CG2 A:THR209 3.3 23.5 1.0
CA A:THR209 3.4 19.2 1.0
C A:ACT908 3.5 46.2 1.0
CH3 A:ACT908 3.8 37.6 1.0
N A:THR209 4.0 17.9 1.0
CB A:ASP171 4.0 19.7 1.0
OD1 A:ASP311 4.1 21.7 1.0
ND1 A:HIS359 4.1 17.8 1.0
CG A:HIS359 4.1 17.6 1.0
N A:GLY172 4.2 16.9 1.0
CA A:ASP171 4.3 20.1 1.0
CB A:ASP358 4.4 18.1 1.0
O A:HOH1003 4.4 28.2 1.0
CE1 A:HIS474 4.4 19.8 1.0
CG A:ASP311 4.4 22.6 1.0
OXT A:ACT908 4.5 32.1 1.0
ZN A:ZN902 4.5 21.4 1.0
NE2 A:HIS474 4.5 19.5 1.0
C A:ASP171 4.6 18.2 1.0
C A:LYS208 4.8 18.8 1.0
C A:THR209 4.8 18.1 1.0
CB A:ASP311 4.8 21.4 1.0
OD2 A:ASP311 4.9 26.5 1.0
CA A:GLY172 4.9 19.0 1.0

Calcium binding site 2 out of 2 in 7g3n

Go back to Calcium Binding Sites List in 7g3n
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-Hydroxy-6-Methyl- 1-Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CC1(O) CC2(CCN2C(=O)C3CNC(N[C@@H]4CC5CCC(Cl)CC5C4)NC3)C1 with IC50=0.0155951 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-Hydroxy-6-Methyl- 1-Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CC1(O) CC2(CCN2C(=O)C3CNC(N[C@@H]4CC5CCC(Cl)CC5C4)NC3)C1 with IC50=0.0155951 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:17.2
occ:1.00
 OD1 A:ASP747 2.2 17.4 1.0
OD1 A:ASP739 2.3 17.2 1.0
OD1 A:ASN741 2.3 19.7 1.0
O A:HOH1433 2.3 21.3 1.0
O A:LEU745 2.3 16.7 1.0
OD1 A:ASP743 2.4 18.3 1.0
CG A:ASP743 3.3 19.9 1.0
CG A:ASN741 3.3 22.9 1.0
CG A:ASP739 3.4 17.9 1.0
CG A:ASP747 3.5 16.4 1.0
C A:LEU745 3.5 17.3 1.0
OD2 A:ASP743 3.7 21.5 1.0
ND2 A:ASN741 3.8 24.1 1.0
CA A:ASP739 3.9 16.1 1.0
N A:ASP747 4.0 16.1 1.0
N A:LEU745 4.0 15.7 1.0
C A:ARG746 4.1 18.4 1.0
CA A:ASP747 4.1 16.5 1.0
CB A:ASP739 4.1 16.3 1.0
CA A:LEU745 4.2 16.1 1.0
O A:ARG746 4.2 17.4 1.0
N A:ASP743 4.3 17.2 1.0
OD2 A:ASP739 4.3 17.0 1.0
OD2 A:ASP747 4.3 19.4 1.0
CB A:ASP747 4.4 16.9 1.0
O A:PHE738 4.5 16.4 1.0
N A:ASN741 4.5 17.5 1.0
C A:ASP739 4.5 16.7 1.0
CB A:LEU745 4.5 18.2 1.0
N A:ARG746 4.5 16.8 1.0
CB A:ASP743 4.5 19.4 1.0
OE2 A:GLU751 4.6 36.7 1.0
CB A:ASN741 4.6 21.6 1.0
O A:HOH1429 4.7 36.3 1.0
N A:TYR740 4.7 17.8 1.0
CA A:ARG746 4.8 18.1 1.0
N A:TYR742 4.8 19.4 1.0
C A:ASN741 4.8 18.9 1.0
N A:GLY744 4.8 18.6 1.0
CA A:ASP743 4.8 18.8 1.0
CA A:ASN741 4.9 18.0 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: Wed Jul 9 22:21:52 2025

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