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Calcium in PDB 7g2v: Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]-2,3-Difluorobenzenesulfonamide, I.E. Smiles C1(C(C(C(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl) C(C)(C)C)F)F)S(=O)(=O)N with IC50=0.0130576 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]-2,3-Difluorobenzenesulfonamide, I.E. Smiles C1(C(C(C(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl) C(C)(C)C)F)F)S(=O)(=O)N with IC50=0.0130576 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]-2,3-Difluorobenzenesulfonamide, I.E. Smiles C1(C(C(C(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl) C(C)(C)C)F)F)S(=O)(=O)N with IC50=0.0130576 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]-2,3-Difluorobenzenesulfonamide, I.E. Smiles C1(C(C(C(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl) C(C)(C)C)F)F)S(=O)(=O)N with IC50=0.0130576 Microm, PDB code: 7g2v 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) 48.61 / 1.52
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.815, 91.549, 119.348, 90, 90, 90
R / Rfree (%) 18 / 21.2

Other elements in 7g2v:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]-2,3-Difluorobenzenesulfonamide, I.E. Smiles C1(C(C(C(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl) C(C)(C)C)F)F)S(=O)(=O)N with IC50=0.0130576 Microm also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]-2,3-Difluorobenzenesulfonamide, I.E. Smiles C1(C(C(C(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl) C(C)(C)C)F)F)S(=O)(=O)N with IC50=0.0130576 Microm (pdb code 7g2v). 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-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]-2,3-Difluorobenzenesulfonamide, I.E. Smiles C1(C(C(C(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl) C(C)(C)C)F)F)S(=O)(=O)N with IC50=0.0130576 Microm, PDB code: 7g2v:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g2v

Go back to Calcium Binding Sites List in 7g2v
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]-2,3-Difluorobenzenesulfonamide, I.E. Smiles C1(C(C(C(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl) C(C)(C)C)F)F)S(=O)(=O)N with IC50=0.0130576 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-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]-2,3-Difluorobenzenesulfonamide, I.E. Smiles C1(C(C(C(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl) C(C)(C)C)F)F)S(=O)(=O)N with IC50=0.0130576 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:37.7
occ:1.00
 OG1 A:THR209 1.7 25.4 1.0
OD1 A:ASP171 2.0 25.2 1.0
NE2 A:HIS359 2.1 20.2 1.0
OD2 A:ASP358 2.4 29.5 1.0
CG A:ASP171 2.6 23.9 1.0
OD2 A:ASP171 2.6 32.4 1.0
O36 A:XIV901 2.8 34.5 1.0
CB A:THR209 2.8 24.0 1.0
CE1 A:HIS359 3.0 20.6 1.0
CD2 A:HIS359 3.0 20.1 1.0
CG A:ASP358 3.2 24.5 1.0
CA A:THR209 3.3 19.5 1.0
CG2 A:THR209 3.3 25.4 1.0
OD1 A:ASP358 3.4 20.7 1.0
N A:THR209 3.7 19.5 1.0
S35 A:XIV901 3.8 40.2 1.0
CB A:ASP171 4.0 20.6 1.0
C6 A:XIV901 4.0 36.7 1.0
O37 A:XIV901 4.0 30.1 1.0
ND1 A:HIS359 4.1 19.5 1.0
C1 A:XIV901 4.1 38.8 1.0
CG A:HIS359 4.1 18.9 1.0
OD1 A:ASP311 4.1 24.2 1.0
N A:GLY172 4.3 20.1 1.0
CE1 A:HIS474 4.3 21.7 1.0
CA A:ASP171 4.4 20.6 1.0
ZN A:ZN906 4.4 22.1 1.0
CB A:ASP358 4.5 18.5 1.0
CG A:ASP311 4.5 22.2 1.0
C A:LYS208 4.6 20.1 1.0
NE2 A:HIS474 4.6 19.8 1.0
C A:ASP171 4.7 21.7 1.0
C A:THR209 4.7 19.5 1.0
OD2 A:ASP311 4.9 23.6 1.0
CB A:ASP311 4.9 20.7 1.0
C5 A:XIV901 4.9 43.5 1.0
OH A:TYR306 5.0 27.8 1.0

Calcium binding site 2 out of 2 in 7g2v

Go back to Calcium Binding Sites List in 7g2v
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]-2,3-Difluorobenzenesulfonamide, I.E. Smiles C1(C(C(C(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl) C(C)(C)C)F)F)S(=O)(=O)N with IC50=0.0130576 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-[3-[(2-Tert- Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8-Tetrahydro-1H- Pyrazolo[3,4-D]Azepine-6-Carbonyl]-2,3-Difluorobenzenesulfonamide, I.E. Smiles C1(C(C(C(CC1)C(=O)N1CCC2=C(CC1)Nn=C2OCC1C(Cc(C(C1)C)Cl) C(C)(C)C)F)F)S(=O)(=O)N with IC50=0.0130576 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:18.3
occ:1.00
 OD1 A:ASP739 2.3 17.3 1.0
OD1 A:ASP747 2.3 20.1 1.0
O A:LEU745 2.3 16.7 1.0
OD1 A:ASN741 2.3 21.2 1.0
OD1 A:ASP743 2.4 19.9 1.0
O A:HOH1391 2.4 22.4 1.0
CG A:ASP743 3.3 20.1 1.0
CG A:ASN741 3.4 23.8 1.0
CG A:ASP739 3.4 17.0 1.0
C A:LEU745 3.5 17.7 1.0
CG A:ASP747 3.5 17.9 1.0
OD2 A:ASP743 3.7 23.2 1.0
ND2 A:ASN741 3.8 25.3 1.0
N A:ASP747 3.9 16.5 1.0
CA A:ASP739 3.9 17.1 1.0
C A:ARG746 4.1 18.0 1.0
N A:LEU745 4.1 17.1 1.0
CA A:ASP747 4.1 17.3 1.0
CB A:ASP739 4.2 17.6 1.0
O A:ARG746 4.2 18.0 1.0
CA A:LEU745 4.2 17.2 1.0
N A:ASP743 4.3 18.7 1.0
OD2 A:ASP747 4.4 19.5 1.0
OD2 A:ASP739 4.4 16.8 1.0
CB A:ASP747 4.4 17.0 1.0
CB A:LEU745 4.5 17.6 1.0
O A:PHE738 4.5 16.5 1.0
C A:ASP739 4.5 18.4 1.0
N A:ASN741 4.5 18.5 1.0
CB A:ASP743 4.5 20.8 1.0
N A:ARG746 4.5 18.9 1.0
OE2 A:GLU751 4.6 29.1 1.0
O A:HOH1380 4.7 28.1 1.0
CB A:ASN741 4.7 21.7 1.0
N A:TYR740 4.7 18.0 1.0
CA A:ARG746 4.7 19.4 1.0
N A:TYR742 4.8 19.5 1.0
CA A:ASP743 4.8 18.5 1.0
C A:ASN741 4.8 20.5 1.0
CA A:ASN741 4.9 20.1 1.0
N A:GLY744 4.9 18.5 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 15:35:09 2025

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