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Calcium in PDB 7g2t: Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[3-[(2-Tert-Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8- Tetrahydro-1H-Pyrazolo[3,4-D]Azepin-6-Yl]Methanone, I.E. Smiles C12C(Cc(CC1)C(=O)N1CCC3=C(CC1)Nn=C3OCC1C(Cc(C(C1)C)Cl)C(C)(C)C)N=NN2 with IC50=0.295297 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[3-[(2-Tert-Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8- Tetrahydro-1H-Pyrazolo[3,4-D]Azepin-6-Yl]Methanone, I.E. Smiles C12C(Cc(CC1)C(=O)N1CCC3=C(CC1)Nn=C3OCC1C(Cc(C(C1)C)Cl)C(C)(C)C)N=NN2 with IC50=0.295297 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[3-[(2-Tert-Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8- Tetrahydro-1H-Pyrazolo[3,4-D]Azepin-6-Yl]Methanone, I.E. Smiles C12C(Cc(CC1)C(=O)N1CCC3=C(CC1)Nn=C3OCC1C(Cc(C(C1)C)Cl)C(C)(C)C)N=NN2 with IC50=0.295297 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[3-[(2-Tert-Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8- Tetrahydro-1H-Pyrazolo[3,4-D]Azepin-6-Yl]Methanone, I.E. Smiles C12C(Cc(CC1)C(=O)N1CCC3=C(CC1)Nn=C3OCC1C(Cc(C(C1)C)Cl)C(C)(C)C)N=NN2 with IC50=0.295297 Microm, PDB code: 7g2t 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) 45.51 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.605, 91.023, 117.171, 90, 90, 90
R / Rfree (%) 17.6 / 20.6

Other elements in 7g2t:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[3-[(2-Tert-Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8- Tetrahydro-1H-Pyrazolo[3,4-D]Azepin-6-Yl]Methanone, I.E. Smiles C12C(Cc(CC1)C(=O)N1CCC3=C(CC1)Nn=C3OCC1C(Cc(C(C1)C)Cl)C(C)(C)C)N=NN2 with IC50=0.295297 Microm also contains other interesting chemical elements:

Potassium (K) 1 atom
Chlorine (Cl) 3 atoms
Zinc (Zn) 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 1H-Benzotriazol-5- Yl-[3-[(2-Tert-Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8- Tetrahydro-1H-Pyrazolo[3,4-D]Azepin-6-Yl]Methanone, I.E. Smiles C12C(Cc(CC1)C(=O)N1CCC3=C(CC1)Nn=C3OCC1C(Cc(C(C1)C)Cl)C(C)(C)C)N=NN2 with IC50=0.295297 Microm (pdb code 7g2t). 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 1H-Benzotriazol-5- Yl-[3-[(2-Tert-Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8- Tetrahydro-1H-Pyrazolo[3,4-D]Azepin-6-Yl]Methanone, I.E. Smiles C12C(Cc(CC1)C(=O)N1CCC3=C(CC1)Nn=C3OCC1C(Cc(C(C1)C)Cl)C(C)(C)C)N=NN2 with IC50=0.295297 Microm, PDB code: 7g2t:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g2t

Go back to Calcium Binding Sites List in 7g2t
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[3-[(2-Tert-Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8- Tetrahydro-1H-Pyrazolo[3,4-D]Azepin-6-Yl]Methanone, I.E. Smiles C12C(Cc(CC1)C(=O)N1CCC3=C(CC1)Nn=C3OCC1C(Cc(C(C1)C)Cl)C(C)(C)C)N=NN2 with IC50=0.295297 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 1H-Benzotriazol-5- Yl-[3-[(2-Tert-Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8- Tetrahydro-1H-Pyrazolo[3,4-D]Azepin-6-Yl]Methanone, I.E. Smiles C12C(Cc(CC1)C(=O)N1CCC3=C(CC1)Nn=C3OCC1C(Cc(C(C1)C)Cl)C(C)(C)C)N=NN2 with IC50=0.295297 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:39.0
occ:1.00
 OD1 A:ASP171 1.8 24.2 1.0
OG1 A:THR209 1.9 25.5 1.0
NE2 A:HIS359 2.2 18.5 1.0
OD2 A:ASP358 2.4 23.6 1.0
CG A:ASP171 2.7 26.3 1.0
CB A:THR209 2.9 20.1 1.0
OD2 A:ASP171 2.9 36.8 1.0
CE1 A:HIS359 3.0 18.5 1.0
CG2 A:THR209 3.1 22.4 1.0
CG A:ASP358 3.2 20.9 1.0
CD2 A:HIS359 3.2 17.4 1.0
CA A:THR209 3.4 17.5 1.0
OD1 A:ASP358 3.5 19.0 1.0
OD2 A:ASP311 3.9 21.3 1.0
N35 A:XUO902 3.9 42.2 1.0
N A:THR209 4.0 17.4 1.0
CB A:ASP171 4.0 20.3 1.0
C1 A:XUO902 4.0 41.1 1.0
ND1 A:HIS359 4.1 18.3 1.0
C6 A:XUO902 4.1 39.0 1.0
CE1 A:HIS474 4.2 18.1 1.0
CG A:HIS359 4.2 16.5 1.0
ZN A:ZN907 4.3 20.8 1.0
N A:GLY172 4.3 16.7 1.0
CA A:ASP171 4.3 20.2 1.0
CG A:ASP311 4.3 19.7 1.0
CB A:ASP358 4.4 18.3 1.0
NE2 A:HIS474 4.5 18.1 1.0
O A:HOH1003 4.5 31.6 1.0
N34 A:XUO902 4.7 41.1 1.0
C A:ASP171 4.7 19.9 1.0
C A:THR209 4.7 15.9 1.0
CB A:ASP311 4.8 18.3 1.0
C2 A:XUO902 4.8 45.5 1.0
OD1 A:ASP311 4.9 23.8 1.0
C A:LYS208 4.9 20.7 1.0
C5 A:XUO902 4.9 40.0 1.0
ND1 A:HIS474 5.0 18.7 1.0
OH A:TYR306 5.0 27.2 1.0

Calcium binding site 2 out of 2 in 7g2t

Go back to Calcium Binding Sites List in 7g2t
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[3-[(2-Tert-Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8- Tetrahydro-1H-Pyrazolo[3,4-D]Azepin-6-Yl]Methanone, I.E. Smiles C12C(Cc(CC1)C(=O)N1CCC3=C(CC1)Nn=C3OCC1C(Cc(C(C1)C)Cl)C(C)(C)C)N=NN2 with IC50=0.295297 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 1H-Benzotriazol-5- Yl-[3-[(2-Tert-Butyl-4-Chloro-5-Methylphenyl)Methoxy]-4,5,7,8- Tetrahydro-1H-Pyrazolo[3,4-D]Azepin-6-Yl]Methanone, I.E. Smiles C12C(Cc(CC1)C(=O)N1CCC3=C(CC1)Nn=C3OCC1C(Cc(C(C1)C)Cl)C(C)(C)C)N=NN2 with IC50=0.295297 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca909

b:17.4
occ:1.00
 O A:LEU745 2.2 15.6 1.0
OD1 A:ASP739 2.3 17.1 1.0
OD1 A:ASN741 2.3 18.4 1.0
OD1 A:ASP747 2.3 17.3 1.0
OD1 A:ASP743 2.3 19.4 1.0
O A:HOH1375 2.4 21.0 1.0
CG A:ASP743 3.3 17.9 1.0
CG A:ASN741 3.4 19.5 1.0
C A:LEU745 3.4 17.0 1.0
CG A:ASP739 3.4 15.4 1.0
CG A:ASP747 3.5 19.1 1.0
OD2 A:ASP743 3.7 20.5 1.0
ND2 A:ASN741 3.8 23.4 1.0
N A:ASP747 3.9 18.1 1.0
CA A:ASP739 3.9 15.6 1.0
C A:ARG746 4.0 18.6 1.0
N A:LEU745 4.1 17.0 1.0
CA A:ASP747 4.1 17.1 1.0
CB A:ASP739 4.2 15.1 1.0
CA A:LEU745 4.2 16.6 1.0
O A:ARG746 4.2 18.1 1.0
N A:ASP743 4.3 18.0 1.0
OD2 A:ASP739 4.4 18.0 1.0
OD2 A:ASP747 4.4 19.2 1.0
CB A:ASP747 4.4 18.8 1.0
CB A:LEU745 4.4 17.9 1.0
O A:PHE738 4.5 16.7 1.0
N A:ARG746 4.5 17.7 1.0
C A:ASP739 4.5 17.9 1.0
N A:ASN741 4.5 17.9 1.0
CB A:ASP743 4.5 19.1 1.0
O A:HOH1339 4.5 33.4 1.0
OE2 A:GLU751 4.6 27.9 1.0
CB A:ASN741 4.6 19.4 1.0
N A:TYR740 4.7 18.2 1.0
CA A:ARG746 4.7 16.6 1.0
N A:TYR742 4.7 18.8 1.0
CA A:ASP743 4.8 17.0 1.0
CA A:ASN741 4.9 18.4 1.0
C A:ASN741 4.9 17.6 1.0
N A:GLY744 4.9 17.1 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: Sat Feb 8 15:35:09 2025

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