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Calcium in PDB 7g3t: Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm, PDB code: 7g3t 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) 72.92 / 1.33
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.77, 91.69, 120.29, 90, 90, 90
R / Rfree (%) 13.5 / 17.2

Other elements in 7g3t:

The structure of Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
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 (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm (pdb code 7g3t). 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 (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm, PDB code: 7g3t:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g3t

Go back to Calcium Binding Sites List in 7g3t
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 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 (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:11.8
occ:1.00
 O A:LEU745 2.3 11.9 1.0
OD1 A:ASN741 2.3 12.5 1.0
OD1 A:ASP747 2.3 12.3 1.0
OD1 A:ASP739 2.3 11.2 1.0
O A:HOH1534 2.3 16.0 1.0
OD1 A:ASP743 2.4 12.1 1.0
CG A:ASP743 3.3 14.5 1.0
CG A:ASN741 3.4 12.4 1.0
C A:LEU745 3.5 10.7 1.0
CG A:ASP739 3.5 10.3 1.0
CG A:ASP747 3.6 10.7 1.0
OD2 A:ASP743 3.8 17.7 1.0
ND2 A:ASN741 3.9 20.2 1.0
CA A:ASP739 3.9 10.1 1.0
N A:ASP747 4.0 11.6 1.0
C A:ARG746 4.1 12.4 1.0
N A:LEU745 4.1 11.1 1.0
CA A:ASP747 4.1 11.9 1.0
CB A:ASP739 4.2 10.1 1.0
CA A:LEU745 4.2 11.2 1.0
O A:ARG746 4.2 12.6 1.0
N A:ASP743 4.3 12.8 1.0
OD2 A:ASP739 4.4 10.9 1.0
CB A:ASP747 4.4 11.9 1.0
OD2 A:ASP747 4.4 12.5 1.0
C A:ASP739 4.4 10.8 1.0
O A:PHE738 4.4 11.5 1.0
CB A:LEU745 4.5 12.1 1.0
N A:ASN741 4.5 11.9 1.0
CB A:ASP743 4.5 13.8 1.0
N A:ARG746 4.5 11.3 1.0
OE2 A:GLU751 4.5 22.6 1.0
O A:HOH1502 4.7 23.1 1.0
CB A:ASN741 4.7 13.4 1.0
CA A:ARG746 4.7 11.7 0.3
N A:TYR742 4.7 12.0 1.0
N A:TYR740 4.7 11.2 1.0
CA A:ARG746 4.8 11.8 0.7
CA A:ASP743 4.8 12.1 1.0
C A:ASN741 4.8 12.2 1.0
N A:GLY744 4.9 11.2 1.0
CA A:ASN741 4.9 11.9 1.0
C A:ASP743 5.0 11.6 1.0

Calcium binding site 2 out of 2 in 7g3t

Go back to Calcium Binding Sites List in 7g3t
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 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 (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:36.2
occ:1.00
 OD1 A:ASP171 1.7 16.7 1.0
OG1 A:THR209 1.8 14.4 1.0
NE2 A:HIS359 2.0 12.5 1.0
OD2 A:ASP358 2.3 16.3 1.0
CG A:ASP171 2.8 14.7 1.0
CB A:THR209 2.8 13.2 1.0
CE1 A:HIS359 2.9 13.3 1.0
CD2 A:HIS359 3.1 11.5 1.0
CG2 A:THR209 3.1 16.1 1.0
CG A:ASP358 3.1 12.4 1.0
CA A:THR209 3.3 11.5 1.0
OD2 A:ASP171 3.4 21.2 1.0
OD1 A:ASP358 3.4 12.2 1.0
O A:HOH1118 3.5 22.7 1.0
N A:THR209 3.9 11.5 1.0
ND1 A:HIS359 4.0 12.6 1.0
CB A:ASP171 4.0 12.9 1.0
OD1 A:ASP311 4.0 19.4 1.0
CG A:HIS359 4.1 11.9 1.0
N A:GLY172 4.2 11.3 1.0
CA A:ASP171 4.3 11.4 1.0
CB A:ASP358 4.4 11.3 1.0
CE1 A:HIS474 4.4 12.0 1.0
CG A:ASP311 4.4 15.0 1.0
ZN A:ZN902 4.5 13.6 1.0
NE2 A:HIS474 4.6 11.5 1.0
O A:ACT908 4.6 21.8 1.0
C A:ASP171 4.6 11.2 1.0
C A:THR209 4.6 10.9 1.0
O A:HOH1003 4.7 8.8 0.5
C A:LYS208 4.7 11.6 1.0
CB A:ASP311 4.8 12.1 1.0
OH A:TYR306 4.8 18.5 1.0
OD2 A:ASP311 4.8 19.6 1.0
CA A:GLY172 5.0 11.7 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: Wed Jul 9 22:22:32 2025

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