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Calcium in PDB 7g3d: Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm, PDB code: 7g3d 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) 48.83 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.23, 91.79, 119.85, 90, 90, 90
R / Rfree (%) 17.7 / 21.8

Other elements in 7g3d:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 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 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm (pdb code 7g3d). 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 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm, PDB code: 7g3d:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g3d

Go back to Calcium Binding Sites List in 7g3d
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 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 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:30.3
occ:1.00
 OD1 A:ASP171 2.0 28.6 1.0
OG1 A:THR209 2.0 23.3 1.0
NE2 A:HIS359 2.2 22.1 1.0
OD2 A:ASP358 2.2 24.9 1.0
CG A:ASP171 2.7 27.8 1.0
OD2 A:ASP171 2.8 37.0 1.0
CB A:THR209 3.0 23.2 1.0
CG A:ASP358 3.0 22.1 1.0
CE1 A:HIS359 3.1 21.5 1.0
CD2 A:HIS359 3.2 21.2 1.0
CG2 A:THR209 3.3 24.3 1.0
OD1 A:ASP358 3.3 21.7 1.0
O1 A:SO4903 3.4 76.6 1.0
CA A:THR209 3.4 22.1 1.0
O A:HOH1014 3.6 43.4 1.0
N A:THR209 3.9 21.9 1.0
CB A:ASP171 4.0 25.4 1.0
ND1 A:HIS359 4.1 21.0 1.0
OD1 A:ASP311 4.2 24.0 1.0
CG A:HIS359 4.2 19.9 1.0
N A:GLY172 4.2 21.9 1.0
CA A:ASP171 4.3 22.8 1.0
O A:HOH1002 4.4 33.4 1.0
CB A:ASP358 4.4 20.9 1.0
CE1 A:HIS474 4.4 21.9 1.0
CG A:ASP311 4.5 22.9 1.0
ZN A:ZN909 4.6 27.4 1.0
NE2 A:HIS474 4.6 21.9 1.0
C A:ASP171 4.7 22.1 1.0
C A:THR209 4.7 22.1 1.0
C A:LYS208 4.7 22.9 1.0
S A:SO4903 4.8 80.0 1.0
CB A:ASP311 4.8 22.7 1.0
OD2 A:ASP311 4.9 24.9 1.0

Calcium binding site 2 out of 2 in 7g3d

Go back to Calcium Binding Sites List in 7g3d
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 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 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca911

b:21.6
occ:1.00
 OD1 A:ASP739 2.3 19.9 1.0
OD1 A:ASP747 2.3 20.6 1.0
OD1 A:ASP743 2.3 25.8 1.0
OD1 A:ASN741 2.3 23.5 1.0
O A:LEU745 2.3 19.5 1.0
O A:HOH1374 2.3 24.9 1.0
CG A:ASP743 3.3 23.6 1.0
CG A:ASN741 3.4 26.4 1.0
CG A:ASP739 3.5 21.4 1.0
C A:LEU745 3.5 21.1 1.0
CG A:ASP747 3.5 22.0 1.0
OD2 A:ASP743 3.7 26.6 1.0
ND2 A:ASN741 3.8 28.6 1.0
CA A:ASP739 3.9 19.7 1.0
N A:ASP747 4.0 19.7 1.0
N A:LEU745 4.1 20.1 1.0
C A:ARG746 4.1 20.1 1.0
O A:ARG746 4.2 20.4 1.0
CB A:ASP739 4.2 19.9 1.0
CA A:LEU745 4.2 20.5 1.0
CA A:ASP747 4.2 20.1 1.0
N A:ASP743 4.3 21.9 1.0
OD2 A:ASP747 4.4 23.7 1.0
OD2 A:ASP739 4.4 21.9 1.0
N A:ASN741 4.4 21.5 1.0
CB A:LEU745 4.5 23.6 1.0
O A:PHE738 4.5 18.1 1.0
C A:ASP739 4.5 20.5 1.0
CB A:ASP747 4.5 20.1 1.0
N A:ARG746 4.5 21.2 1.0
CB A:ASP743 4.5 21.9 1.0
OE2 A:GLU751 4.7 33.0 1.0
CB A:ASN741 4.7 23.0 1.0
N A:TYR740 4.7 22.1 1.0
N A:TYR742 4.8 22.5 1.0
CA A:ARG746 4.8 22.0 1.0
CA A:ASP743 4.8 21.2 1.0
O A:HOH1365 4.8 43.2 1.0
C A:ASN741 4.9 23.3 1.0
N A:GLY744 4.9 20.7 1.0
CA A:ASN741 4.9 23.1 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 22:20:03 2025

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