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Calcium in PDB 7g3s: Crystal Structure of Rat Autotaxin in Complex with 2-[(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)Amino]-6-(Oxetan-3-Yl)-7H-Pyrrolo[3,4- D]Pyrimidin-5-One, I.E. Smiles O=C1N(C2COC2)CC2NC(N[C@H]3CC4C(C3) Ccc(C4)Cl)NCC12 with IC50=0.150181 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)Amino]-6-(Oxetan-3-Yl)-7H-Pyrrolo[3,4- D]Pyrimidin-5-One, I.E. Smiles O=C1N(C2COC2)CC2NC(N[C@H]3CC4C(C3) Ccc(C4)Cl)NCC12 with IC50=0.150181 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)Amino]-6-(Oxetan-3-Yl)-7H-Pyrrolo[3,4- D]Pyrimidin-5-One, I.E. Smiles O=C1N(C2COC2)CC2NC(N[C@H]3CC4C(C3) Ccc(C4)Cl)NCC12 with IC50=0.150181 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)Amino]-6-(Oxetan-3-Yl)-7H-Pyrrolo[3,4- D]Pyrimidin-5-One, I.E. Smiles O=C1N(C2COC2)CC2NC(N[C@H]3CC4C(C3) Ccc(C4)Cl)NCC12 with IC50=0.150181 Microm, PDB code: 7g3s 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) 73.10 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.17, 92.208, 119.918, 90, 90, 90
R / Rfree (%) 16.9 / 22.4

Other elements in 7g3s:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)Amino]-6-(Oxetan-3-Yl)-7H-Pyrrolo[3,4- D]Pyrimidin-5-One, I.E. Smiles O=C1N(C2COC2)CC2NC(N[C@H]3CC4C(C3) Ccc(C4)Cl)NCC12 with IC50=0.150181 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 2-[(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)Amino]-6-(Oxetan-3-Yl)-7H-Pyrrolo[3,4- D]Pyrimidin-5-One, I.E. Smiles O=C1N(C2COC2)CC2NC(N[C@H]3CC4C(C3) Ccc(C4)Cl)NCC12 with IC50=0.150181 Microm (pdb code 7g3s). 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-[(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)Amino]-6-(Oxetan-3-Yl)-7H-Pyrrolo[3,4- D]Pyrimidin-5-One, I.E. Smiles O=C1N(C2COC2)CC2NC(N[C@H]3CC4C(C3) Ccc(C4)Cl)NCC12 with IC50=0.150181 Microm, PDB code: 7g3s:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g3s

Go back to Calcium Binding Sites List in 7g3s
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)Amino]-6-(Oxetan-3-Yl)-7H-Pyrrolo[3,4- D]Pyrimidin-5-One, I.E. Smiles O=C1N(C2COC2)CC2NC(N[C@H]3CC4C(C3) Ccc(C4)Cl)NCC12 with IC50=0.150181 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-[(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)Amino]-6-(Oxetan-3-Yl)-7H-Pyrrolo[3,4- D]Pyrimidin-5-One, I.E. Smiles O=C1N(C2COC2)CC2NC(N[C@H]3CC4C(C3) Ccc(C4)Cl)NCC12 with IC50=0.150181 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:39.0
occ:1.00
 OG1 A:THR209 1.9 21.4 1.0
OD1 A:ASP171 1.9 24.5 1.0
NE2 A:HIS359 2.0 17.1 1.0
OD2 A:ASP358 2.5 20.3 1.0
CE1 A:HIS359 2.9 18.0 1.0
CB A:THR209 2.9 20.8 1.0
CG A:ASP171 2.9 22.5 1.0
CD2 A:HIS359 3.0 16.8 1.0
CG2 A:THR209 3.2 19.9 1.0
O A:HOH1012 3.2 40.6 1.0
CA A:THR209 3.3 20.9 1.0
CG A:ASP358 3.3 19.7 1.0
OD2 A:ASP171 3.3 28.9 1.0
OD1 A:ASP358 3.5 18.6 1.0
N A:THR209 3.9 21.2 1.0
ND1 A:HIS359 4.0 18.0 1.0
CG A:HIS359 4.1 17.2 1.0
OD1 A:ASP311 4.1 19.5 1.0
CB A:ASP171 4.2 21.0 1.0
CE1 A:HIS474 4.2 20.2 1.0
O A:HOH1004 4.3 26.5 1.0
N A:GLY172 4.4 19.3 1.0
NE2 A:HIS474 4.4 18.9 1.0
ZN A:ZN905 4.4 21.2 1.0
CG A:ASP311 4.5 19.3 1.0
CA A:ASP171 4.5 19.8 1.0
CB A:ASP358 4.5 19.7 1.0
C A:THR209 4.6 21.8 1.0
O A:HOH1427 4.6 24.2 1.0
C A:LYS208 4.6 20.5 1.0
C A:ASP171 4.8 20.2 1.0
OD2 A:ASP311 4.9 20.2 1.0
ND1 A:HIS474 4.9 18.6 1.0
CB A:ASP311 5.0 19.6 1.0

Calcium binding site 2 out of 2 in 7g3s

Go back to Calcium Binding Sites List in 7g3s
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)Amino]-6-(Oxetan-3-Yl)-7H-Pyrrolo[3,4- D]Pyrimidin-5-One, I.E. Smiles O=C1N(C2COC2)CC2NC(N[C@H]3CC4C(C3) Ccc(C4)Cl)NCC12 with IC50=0.150181 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-[(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)Amino]-6-(Oxetan-3-Yl)-7H-Pyrrolo[3,4- D]Pyrimidin-5-One, I.E. Smiles O=C1N(C2COC2)CC2NC(N[C@H]3CC4C(C3) Ccc(C4)Cl)NCC12 with IC50=0.150181 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:17.9
occ:1.00
 OD1 A:ASP743 2.3 19.6 1.0
OD1 A:ASN741 2.3 20.4 1.0
O A:HOH1394 2.3 20.4 1.0
OD1 A:ASP739 2.3 19.2 1.0
O A:LEU745 2.3 18.4 1.0
OD1 A:ASP747 2.3 18.6 1.0
CG A:ASP743 3.3 19.8 1.0
CG A:ASN741 3.4 21.1 1.0
C A:LEU745 3.4 19.5 1.0
CG A:ASP739 3.5 19.1 1.0
CG A:ASP747 3.6 19.6 1.0
OD2 A:ASP743 3.9 20.5 1.0
ND2 A:ASN741 3.9 19.5 1.0
CA A:ASP739 3.9 17.6 1.0
N A:ASP747 4.0 19.4 1.0
N A:LEU745 4.1 18.6 1.0
C A:ARG746 4.1 20.5 1.0
CA A:LEU745 4.2 19.2 1.0
CB A:ASP739 4.2 17.7 1.0
CA A:ASP747 4.2 19.3 1.0
O A:ARG746 4.2 21.1 1.0
N A:ASP743 4.3 20.4 1.0
OD2 A:ASP739 4.4 20.3 1.0
N A:ASN741 4.4 19.2 1.0
OD2 A:ASP747 4.4 20.0 1.0
O A:PHE738 4.4 16.6 1.0
CB A:ASP743 4.4 18.0 1.0
CB A:LEU745 4.5 21.2 1.0
C A:ASP739 4.5 18.0 1.0
CB A:ASP747 4.5 19.5 1.0
N A:ARG746 4.5 19.8 1.0
OE2 A:GLU751 4.6 33.9 1.0
CB A:ASN741 4.7 20.1 1.0
N A:TYR740 4.7 19.7 1.0
N A:TYR742 4.7 20.5 1.0
O A:HOH1245 4.8 36.7 1.0
CA A:ASP743 4.8 18.5 1.0
C A:ASN741 4.8 20.7 1.0
CA A:ARG746 4.8 20.1 1.0
CA A:ASN741 4.8 20.2 1.0
N A:GLY744 4.9 17.4 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 22:22:32 2025

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