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Calcium in PDB 7g5z: Crystal Structure of Rat Autotaxin in Complex with N-(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)-6-(5-Methylpyrimidin-2-Yl)-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2-Amine, I.E. Smiles CLC1CC2C(CC1) C[C@@H](C2)NC1NCC2CN(CC2N1)C1NCC(CN1)C with IC50=0.0693825 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with N-(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)-6-(5-Methylpyrimidin-2-Yl)-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2-Amine, I.E. Smiles CLC1CC2C(CC1) C[C@@H](C2)NC1NCC2CN(CC2N1)C1NCC(CN1)C with IC50=0.0693825 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with N-(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)-6-(5-Methylpyrimidin-2-Yl)-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2-Amine, I.E. Smiles CLC1CC2C(CC1) C[C@@H](C2)NC1NCC2CN(CC2N1)C1NCC(CN1)C with IC50=0.0693825 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with N-(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)-6-(5-Methylpyrimidin-2-Yl)-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2-Amine, I.E. Smiles CLC1CC2C(CC1) C[C@@H](C2)NC1NCC2CN(CC2N1)C1NCC(CN1)C with IC50=0.0693825 Microm, PDB code: 7g5z 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) 72.63 / 1.44
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.67, 91.463, 119.489, 90, 90, 90
R / Rfree (%) 17.4 / 19.9

Other elements in 7g5z:

The structure of Crystal Structure of Rat Autotaxin in Complex with N-(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)-6-(5-Methylpyrimidin-2-Yl)-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2-Amine, I.E. Smiles CLC1CC2C(CC1) C[C@@H](C2)NC1NCC2CN(CC2N1)C1NCC(CN1)C with IC50=0.0693825 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 N-(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)-6-(5-Methylpyrimidin-2-Yl)-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2-Amine, I.E. Smiles CLC1CC2C(CC1) C[C@@H](C2)NC1NCC2CN(CC2N1)C1NCC(CN1)C with IC50=0.0693825 Microm (pdb code 7g5z). 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-(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)-6-(5-Methylpyrimidin-2-Yl)-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2-Amine, I.E. Smiles CLC1CC2C(CC1) C[C@@H](C2)NC1NCC2CN(CC2N1)C1NCC(CN1)C with IC50=0.0693825 Microm, PDB code: 7g5z:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g5z

Go back to Calcium Binding Sites List in 7g5z
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with N-(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)-6-(5-Methylpyrimidin-2-Yl)-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2-Amine, I.E. Smiles CLC1CC2C(CC1) C[C@@H](C2)NC1NCC2CN(CC2N1)C1NCC(CN1)C with IC50=0.0693825 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-(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)-6-(5-Methylpyrimidin-2-Yl)-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2-Amine, I.E. Smiles CLC1CC2C(CC1) C[C@@H](C2)NC1NCC2CN(CC2N1)C1NCC(CN1)C with IC50=0.0693825 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:16.5
occ:1.00
 OD1 A:ASP171 1.8 10.6 0.3
OD1 A:ASP171 1.9 15.4 0.7
OG1 A:THR209 1.9 13.2 1.0
NE2 A:HIS359 2.0 12.4 1.0
OD2 A:ASP358 2.2 15.1 1.0
CG A:ASP171 2.6 14.2 0.7
OD2 A:ASP171 2.8 18.4 0.7
CB A:THR209 2.9 13.9 1.0
CG A:ASP171 2.9 11.2 0.3
CE1 A:HIS359 2.9 11.6 1.0
CD2 A:HIS359 3.0 11.2 1.0
CG A:ASP358 3.0 12.6 1.0
CG2 A:THR209 3.2 15.1 1.0
OD1 A:ASP358 3.3 11.4 1.0
CA A:THR209 3.3 11.8 1.0
OD2 A:ASP171 3.5 10.9 0.3
O A:HOH1595 3.7 18.6 0.5
N A:THR209 3.9 11.0 1.0
CB A:ASP171 4.0 13.0 0.7
ND1 A:HIS359 4.0 11.7 1.0
CG A:HIS359 4.0 11.2 1.0
OD1 A:ASP311 4.0 14.8 1.0
CB A:ASP171 4.1 11.4 0.3
N A:GLY172 4.2 11.0 1.0
O A:HOH1139 4.3 22.4 1.0
CB A:ASP358 4.3 10.6 1.0
CA A:ASP171 4.3 11.9 0.3
CA A:ASP171 4.3 12.7 0.7
O A:HOH1639 4.4 21.9 1.0
CE1 A:HIS474 4.4 13.2 1.0
CG A:ASP311 4.4 13.0 1.0
ZN A:ZN1007 4.6 13.2 1.0
NE2 A:HIS474 4.6 11.8 1.0
C A:ASP171 4.6 12.2 1.0
C A:THR209 4.7 12.4 1.0
C A:LYS208 4.7 10.8 1.0
CB A:ASP311 4.9 12.1 1.0
CA A:GLY172 5.0 11.9 1.0

Calcium binding site 2 out of 2 in 7g5z

Go back to Calcium Binding Sites List in 7g5z
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with N-(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)-6-(5-Methylpyrimidin-2-Yl)-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2-Amine, I.E. Smiles CLC1CC2C(CC1) C[C@@H](C2)NC1NCC2CN(CC2N1)C1NCC(CN1)C with IC50=0.0693825 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-(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)-6-(5-Methylpyrimidin-2-Yl)-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2-Amine, I.E. Smiles CLC1CC2C(CC1) C[C@@H](C2)NC1NCC2CN(CC2N1)C1NCC(CN1)C with IC50=0.0693825 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1009

b:9.6
occ:1.00
 OD1 A:ASP747 2.2 10.9 1.0
O A:LEU745 2.3 10.2 1.0
OD1 A:ASN741 2.3 12.4 1.0
OD1 A:ASP739 2.3 10.9 1.0
OD1 A:ASP743 2.4 9.9 1.0
O A:HOH1493 2.4 13.1 1.0
CG A:ASP743 3.3 11.7 1.0
CG A:ASN741 3.4 13.2 1.0
C A:LEU745 3.5 9.5 1.0
CG A:ASP739 3.5 9.6 1.0
CG A:ASP747 3.5 9.7 1.0
OD2 A:ASP743 3.8 14.6 1.0
ND2 A:ASN741 3.8 14.7 1.0
CA A:ASP739 3.9 9.0 1.0
N A:ASP747 3.9 9.5 1.0
N A:LEU745 4.1 9.2 1.0
C A:ARG746 4.1 10.8 1.0
CA A:ASP747 4.1 9.9 1.0
CB A:ASP739 4.2 9.5 1.0
CA A:LEU745 4.2 9.6 1.0
O A:ARG746 4.3 10.5 1.0
N A:ASP743 4.3 10.6 1.0
CB A:ASP747 4.4 9.0 1.0
OD2 A:ASP747 4.4 10.9 1.0
OD2 A:ASP739 4.4 9.6 1.0
O A:PHE738 4.4 9.3 1.0
C A:ASP739 4.5 9.7 1.0
N A:ASN741 4.5 10.8 1.0
N A:ARG746 4.5 9.8 1.0
CB A:LEU745 4.5 10.3 1.0
OE2 A:GLU751 4.5 19.9 1.0
CB A:ASP743 4.5 11.1 1.0
O A:HOH1331 4.6 23.0 1.0
CB A:ASN741 4.7 11.9 1.0
N A:TYR740 4.7 9.4 1.0
N A:TYR742 4.8 11.1 1.0
CA A:ARG746 4.8 10.2 1.0
CA A:ASP743 4.8 11.1 1.0
C A:ASN741 4.8 11.7 1.0
CA A:ASN741 4.9 11.1 1.0
N A:GLY744 4.9 10.7 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 15:53:35 2025

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