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Calcium in PDB 7g2j: Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm, PDB code: 7g2j was solved by M.Stihle, J.Benz, D.Hunziker, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.86 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.275, 91.714, 119.828, 90, 90, 90
R / Rfree (%) 18.2 / 22.1

Other elements in 7g2j:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm (pdb code 7g2j). 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-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm, PDB code: 7g2j:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g2j

Go back to Calcium Binding Sites List in 7g2j
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 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-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:34.0
occ:1.00
 OG1 A:THR209 2.0 26.6 1.0
OD1 A:ASP171 2.1 30.2 1.0
OD2 A:ASP358 2.3 25.3 1.0
NE2 A:HIS359 2.3 24.6 1.0
OD2 A:ASP171 2.6 34.3 1.0
CG A:ASP171 2.6 27.9 1.0
CB A:THR209 3.0 26.4 1.0
CG A:ASP358 3.1 24.4 1.0
CD2 A:HIS359 3.2 23.2 1.0
CE1 A:HIS359 3.2 24.4 1.0
CG2 A:THR209 3.2 27.6 1.0
CA A:THR209 3.4 26.1 1.0
OD1 A:ASP358 3.4 21.5 1.0
O A:HOH1013 3.5 45.2 1.0
N A:THR209 3.9 25.2 1.0
CB A:ASP171 4.0 26.3 1.0
O3 A:SO4904 4.1 51.0 1.0
O1 A:SO4904 4.2 47.4 1.0
ND1 A:HIS359 4.2 24.1 1.0
OD1 A:ASP311 4.3 26.4 1.0
CG A:HIS359 4.3 22.4 1.0
N A:GLY172 4.3 23.7 1.0
CA A:ASP171 4.4 25.6 1.0
CE1 A:HIS474 4.4 23.7 1.0
CB A:ASP358 4.4 23.1 1.0
CG A:ASP311 4.5 25.7 1.0
ZN A:ZN908 4.6 29.1 1.0
NE2 A:HIS474 4.7 27.1 1.0
C A:THR209 4.7 24.4 1.0
S A:SO4904 4.7 80.0 1.0
C A:ASP171 4.7 25.0 1.0
C A:LYS208 4.7 26.2 1.0
OD2 A:ASP311 4.9 27.9 1.0
CB A:ASP311 4.9 23.7 1.0

Calcium binding site 2 out of 2 in 7g2j

Go back to Calcium Binding Sites List in 7g2j
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 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-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-(1H-Pyrazolo[3,4-B]Pyridin-3- Ylmethoxy)Benzonitrile, I.E. Smiles C1C(C1)OC1CCC(F)C(C1)C1CC(C#N) C(Cl)CC1OCC1=NNC2NCCCC12 with IC50=0.0201566 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca910

b:23.2
occ:1.00
 OD1 A:ASP747 2.3 22.0 1.0
OD1 A:ASN741 2.3 25.6 1.0
O A:HOH1322 2.3 27.0 1.0
OD1 A:ASP739 2.3 22.5 1.0
OD1 A:ASP743 2.3 23.9 1.0
O A:LEU745 2.3 23.8 1.0
CG A:ASP743 3.3 25.4 1.0
CG A:ASN741 3.3 26.4 1.0
C A:LEU745 3.5 23.8 1.0
CG A:ASP739 3.5 21.9 1.0
CG A:ASP747 3.5 24.4 1.0
ND2 A:ASN741 3.7 25.7 1.0
OD2 A:ASP743 3.7 29.9 1.0
CA A:ASP739 3.9 21.5 1.0
N A:ASP747 3.9 22.0 1.0
N A:LEU745 4.1 22.3 1.0
C A:ARG746 4.1 22.9 1.0
O A:ARG746 4.2 20.5 1.0
CA A:ASP747 4.2 21.6 1.0
CA A:LEU745 4.2 22.7 1.0
CB A:ASP739 4.2 22.3 1.0
N A:ASP743 4.3 23.9 1.0
OD2 A:ASP747 4.3 26.2 1.0
OD2 A:ASP739 4.4 20.3 1.0
O A:PHE738 4.4 19.8 1.0
CB A:ASP747 4.4 22.7 1.0
CB A:LEU745 4.4 25.9 1.0
C A:ASP739 4.5 23.1 1.0
CB A:ASP743 4.5 23.9 1.0
N A:ASN741 4.5 22.9 1.0
N A:ARG746 4.5 22.9 1.0
OE2 A:GLU751 4.6 37.4 1.0
CB A:ASN741 4.7 23.6 1.0
N A:TYR740 4.7 22.8 1.0
N A:TYR742 4.8 24.9 1.0
CA A:ASP743 4.8 23.4 1.0
CA A:ARG746 4.8 23.0 1.0
C A:ASN741 4.9 25.5 1.0
N A:GLY744 4.9 21.7 1.0
CA A:ASN741 4.9 24.6 1.0
O A:HOH1299 5.0 37.3 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 15:33:32 2025

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