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Calcium in PDB 7g3o: Crystal Structure of Rat Autotaxin in Complex with 1-[2-(2,3-Dihydro- 1H-Inden-2-Ylamino)-5,7-Dihydropyrrolo[3,4-D]Pyrimidin-6-Yl]-2-[2- (1H-Triazol-5-Yl)Ethoxy]Ethanone, I.E. Smiles C12C(CCCC1)Cc(C2) NC1NCC2C(N1)Cn(C2)C(=O)COCCC1=Cn=NN1 with IC50=0.0017376 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1-[2-(2,3-Dihydro- 1H-Inden-2-Ylamino)-5,7-Dihydropyrrolo[3,4-D]Pyrimidin-6-Yl]-2-[2- (1H-Triazol-5-Yl)Ethoxy]Ethanone, I.E. Smiles C12C(CCCC1)Cc(C2) NC1NCC2C(N1)Cn(C2)C(=O)COCCC1=Cn=NN1 with IC50=0.0017376 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1-[2-(2,3-Dihydro- 1H-Inden-2-Ylamino)-5,7-Dihydropyrrolo[3,4-D]Pyrimidin-6-Yl]-2-[2- (1H-Triazol-5-Yl)Ethoxy]Ethanone, I.E. Smiles C12C(CCCC1)Cc(C2) NC1NCC2C(N1)Cn(C2)C(=O)COCCC1=Cn=NN1 with IC50=0.0017376 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 1-[2-(2,3-Dihydro- 1H-Inden-2-Ylamino)-5,7-Dihydropyrrolo[3,4-D]Pyrimidin-6-Yl]-2-[2- (1H-Triazol-5-Yl)Ethoxy]Ethanone, I.E. Smiles C12C(CCCC1)Cc(C2) NC1NCC2C(N1)Cn(C2)C(=O)COCCC1=Cn=NN1 with IC50=0.0017376 Microm, PDB code: 7g3o 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) 72.87 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.94, 91.59, 120.277, 90, 90, 90
R / Rfree (%) 16.9 / 20.9

Other elements in 7g3o:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1-[2-(2,3-Dihydro- 1H-Inden-2-Ylamino)-5,7-Dihydropyrrolo[3,4-D]Pyrimidin-6-Yl]-2-[2- (1H-Triazol-5-Yl)Ethoxy]Ethanone, I.E. Smiles C12C(CCCC1)Cc(C2) NC1NCC2C(N1)Cn(C2)C(=O)COCCC1=Cn=NN1 with IC50=0.0017376 Microm also contains other interesting chemical elements:

Potassium (K) 1 atom
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 1-[2-(2,3-Dihydro- 1H-Inden-2-Ylamino)-5,7-Dihydropyrrolo[3,4-D]Pyrimidin-6-Yl]-2-[2- (1H-Triazol-5-Yl)Ethoxy]Ethanone, I.E. Smiles C12C(CCCC1)Cc(C2) NC1NCC2C(N1)Cn(C2)C(=O)COCCC1=Cn=NN1 with IC50=0.0017376 Microm (pdb code 7g3o). 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 1-[2-(2,3-Dihydro- 1H-Inden-2-Ylamino)-5,7-Dihydropyrrolo[3,4-D]Pyrimidin-6-Yl]-2-[2- (1H-Triazol-5-Yl)Ethoxy]Ethanone, I.E. Smiles C12C(CCCC1)Cc(C2) NC1NCC2C(N1)Cn(C2)C(=O)COCCC1=Cn=NN1 with IC50=0.0017376 Microm, PDB code: 7g3o:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g3o

Go back to Calcium Binding Sites List in 7g3o
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1-[2-(2,3-Dihydro- 1H-Inden-2-Ylamino)-5,7-Dihydropyrrolo[3,4-D]Pyrimidin-6-Yl]-2-[2- (1H-Triazol-5-Yl)Ethoxy]Ethanone, I.E. Smiles C12C(CCCC1)Cc(C2) NC1NCC2C(N1)Cn(C2)C(=O)COCCC1=Cn=NN1 with IC50=0.0017376 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 1-[2-(2,3-Dihydro- 1H-Inden-2-Ylamino)-5,7-Dihydropyrrolo[3,4-D]Pyrimidin-6-Yl]-2-[2- (1H-Triazol-5-Yl)Ethoxy]Ethanone, I.E. Smiles C12C(CCCC1)Cc(C2) NC1NCC2C(N1)Cn(C2)C(=O)COCCC1=Cn=NN1 with IC50=0.0017376 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:28.1
occ:1.00
 OD1 A:ASP171 1.7 17.3 0.5
OG1 A:THR209 1.9 16.9 1.0
OD1 A:ASP171 2.0 17.7 0.5
NE2 A:HIS359 2.1 13.3 1.0
OD2 A:ASP358 2.4 20.4 1.0
CG A:ASP171 2.6 17.1 0.5
OD2 A:ASP171 2.7 16.5 0.5
CG A:ASP171 2.9 18.2 0.5
CB A:THR209 2.9 16.5 1.0
CE1 A:HIS359 2.9 16.6 1.0
CG2 A:THR209 3.1 20.6 1.0
CD2 A:HIS359 3.1 16.4 1.0
CG A:ASP358 3.1 15.8 1.0
CA A:THR209 3.3 15.2 1.0
OD1 A:ASP358 3.4 14.4 1.0
OD2 A:ASP171 3.4 17.4 0.5
N20 A:YOW901 3.7 36.5 0.5
N24 A:YOW901 3.8 36.8 0.5
N A:THR209 3.9 15.4 1.0
CB A:ASP171 4.0 15.2 0.5
ND1 A:HIS359 4.0 13.7 1.0
CG A:HIS359 4.1 13.7 1.0
OD1 A:ASP311 4.1 19.5 1.0
CB A:ASP171 4.1 15.5 0.5
C25 A:YOW901 4.2 39.1 0.5
N24 A:YOW901 4.3 39.7 0.5
CE1 A:HIS474 4.3 15.4 1.0
N A:GLY172 4.3 14.3 1.0
CA A:ASP171 4.3 15.2 0.5
CA A:ASP171 4.3 15.0 0.5
CB A:ASP358 4.4 16.4 1.0
CG A:ASP311 4.5 18.5 1.0
C23 A:YOW901 4.5 45.5 0.5
O A:HOH1004 4.5 7.9 0.5
NE2 A:HIS474 4.5 14.0 1.0
ZN A:ZN902 4.5 18.1 1.0
C A:THR209 4.6 15.7 1.0
C A:ASP171 4.7 14.7 1.0
C A:LYS208 4.7 16.4 1.0
N21 A:YOW901 4.9 29.9 0.5
CB A:ASP311 4.9 16.8 1.0
OD2 A:ASP311 4.9 20.9 1.0
OH A:TYR306 4.9 23.9 1.0

Calcium binding site 2 out of 2 in 7g3o

Go back to Calcium Binding Sites List in 7g3o
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1-[2-(2,3-Dihydro- 1H-Inden-2-Ylamino)-5,7-Dihydropyrrolo[3,4-D]Pyrimidin-6-Yl]-2-[2- (1H-Triazol-5-Yl)Ethoxy]Ethanone, I.E. Smiles C12C(CCCC1)Cc(C2) NC1NCC2C(N1)Cn(C2)C(=O)COCCC1=Cn=NN1 with IC50=0.0017376 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 1-[2-(2,3-Dihydro- 1H-Inden-2-Ylamino)-5,7-Dihydropyrrolo[3,4-D]Pyrimidin-6-Yl]-2-[2- (1H-Triazol-5-Yl)Ethoxy]Ethanone, I.E. Smiles C12C(CCCC1)Cc(C2) NC1NCC2C(N1)Cn(C2)C(=O)COCCC1=Cn=NN1 with IC50=0.0017376 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:13.7
occ:1.00
 OD1 A:ASP739 2.2 14.1 1.0
OD1 A:ASP747 2.3 16.0 1.0
O A:LEU745 2.3 13.6 1.0
OD1 A:ASN741 2.3 17.1 1.0
O A:HOH1437 2.3 18.8 1.0
OD1 A:ASP743 2.3 15.6 1.0
CG A:ASP743 3.3 17.7 1.0
CG A:ASN741 3.4 19.3 1.0
CG A:ASP739 3.4 13.5 1.0
C A:LEU745 3.5 14.3 1.0
CG A:ASP747 3.5 14.8 1.0
OD2 A:ASP743 3.8 19.6 1.0
ND2 A:ASN741 3.9 19.6 1.0
CA A:ASP739 3.9 12.4 1.0
N A:ASP747 4.0 12.7 1.0
C A:ARG746 4.1 14.2 1.0
N A:LEU745 4.1 13.7 1.0
CB A:ASP739 4.2 13.8 1.0
CA A:ASP747 4.2 14.2 1.0
CA A:LEU745 4.2 13.9 1.0
O A:ARG746 4.3 14.9 1.0
N A:ASP743 4.3 15.4 1.0
OD2 A:ASP739 4.3 15.2 1.0
OD2 A:ASP747 4.4 14.8 1.0
CB A:ASP747 4.4 13.3 1.0
O A:PHE738 4.5 11.5 1.0
N A:ASN741 4.5 15.5 1.0
C A:ASP739 4.5 13.7 1.0
N A:ARG746 4.5 14.4 1.0
CB A:ASP743 4.5 17.1 1.0
CB A:LEU745 4.5 14.8 1.0
OE2 A:GLU751 4.6 29.9 1.0
CB A:ASN741 4.7 18.4 1.0
N A:TYR740 4.7 15.2 1.0
CA A:ARG746 4.7 15.1 1.0
N A:TYR742 4.8 15.2 1.0
O A:HOH1451 4.8 31.4 1.0
CA A:ASP743 4.8 14.8 1.0
C A:ASN741 4.9 17.0 1.0
CA A:ASN741 4.9 17.0 1.0
N A:GLY744 4.9 13.7 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 15:38:33 2025

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