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Calcium in PDB 7g3k: Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[(7-Methyl-8-Oxo-5,6-Dihydroimidazo[1,5-A]Pyrazin-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C2N1CCN(C2=O)C)Cl)C#N with IC50=0.416172 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[(7-Methyl-8-Oxo-5,6-Dihydroimidazo[1,5-A]Pyrazin-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C2N1CCN(C2=O)C)Cl)C#N with IC50=0.416172 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[(7-Methyl-8-Oxo-5,6-Dihydroimidazo[1,5-A]Pyrazin-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C2N1CCN(C2=O)C)Cl)C#N with IC50=0.416172 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[(7-Methyl-8-Oxo-5,6-Dihydroimidazo[1,5-A]Pyrazin-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C2N1CCN(C2=O)C)Cl)C#N with IC50=0.416172 Microm, PDB code: 7g3k was solved by M.Stihle, J.Benz, D.Hunziker, L.Green, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.67 / 1.61
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.038, 90.552, 117.24, 90, 90, 90
R / Rfree (%) 16.8 / 20.4

Other elements in 7g3k:

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[(7-Methyl-8-Oxo-5,6-Dihydroimidazo[1,5-A]Pyrazin-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C2N1CCN(C2=O)C)Cl)C#N with IC50=0.416172 Microm also contains other interesting chemical elements:

Potassium (K) 1 atom
Zinc (Zn) 1 atom
Chlorine (Cl) 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 5-Tert-Butyl-2- Chloro-4-[(7-Methyl-8-Oxo-5,6-Dihydroimidazo[1,5-A]Pyrazin-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C2N1CCN(C2=O)C)Cl)C#N with IC50=0.416172 Microm (pdb code 7g3k). 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 5-Tert-Butyl-2- Chloro-4-[(7-Methyl-8-Oxo-5,6-Dihydroimidazo[1,5-A]Pyrazin-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C2N1CCN(C2=O)C)Cl)C#N with IC50=0.416172 Microm, PDB code: 7g3k:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g3k

Go back to Calcium Binding Sites List in 7g3k
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[(7-Methyl-8-Oxo-5,6-Dihydroimidazo[1,5-A]Pyrazin-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C2N1CCN(C2=O)C)Cl)C#N with IC50=0.416172 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 5-Tert-Butyl-2- Chloro-4-[(7-Methyl-8-Oxo-5,6-Dihydroimidazo[1,5-A]Pyrazin-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C2N1CCN(C2=O)C)Cl)C#N with IC50=0.416172 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1007

b:14.8
occ:1.00
 OD1 A:ASP747 2.2 16.7 1.0
OD1 A:ASP739 2.2 14.1 1.0
O A:LEU745 2.3 14.8 1.0
OD1 A:ASN741 2.3 17.1 1.0
OD1 A:ASP743 2.4 16.2 1.0
O A:HOH1439 2.4 17.1 1.0
CG A:ASP743 3.3 18.1 1.0
CG A:ASP739 3.4 13.6 1.0
CG A:ASN741 3.4 18.2 1.0
C A:LEU745 3.4 14.6 1.0
CG A:ASP747 3.5 16.7 1.0
OD2 A:ASP743 3.7 17.7 1.0
ND2 A:ASN741 3.9 22.6 1.0
CA A:ASP739 3.9 13.7 1.0
N A:ASP747 3.9 14.4 1.0
C A:ARG746 4.1 15.7 1.0
N A:LEU745 4.1 15.3 1.0
CB A:ASP739 4.2 14.7 1.0
CA A:ASP747 4.2 15.9 1.0
CA A:LEU745 4.2 15.8 1.0
O A:ARG746 4.3 14.2 1.0
N A:ASP743 4.3 16.4 1.0
OD2 A:ASP739 4.3 13.7 1.0
OD2 A:ASP747 4.3 17.9 1.0
CB A:ASP747 4.4 15.7 1.0
CB A:LEU745 4.4 16.2 1.0
O A:PHE738 4.4 15.6 1.0
N A:ASN741 4.4 16.4 1.0
C A:ASP739 4.5 14.9 1.0
N A:ARG746 4.5 15.2 1.0
CB A:ASP743 4.5 17.8 1.0
CB A:ASN741 4.7 17.0 1.0
N A:TYR740 4.7 14.7 1.0
N A:TYR742 4.7 15.4 1.0
CA A:ARG746 4.7 15.3 1.0
OE2 A:GLU751 4.8 29.0 1.0
CA A:ASP743 4.8 16.5 1.0
C A:ASN741 4.8 17.7 1.0
N A:GLY744 4.8 15.7 1.0
CA A:ASN741 4.9 15.9 1.0

Calcium binding site 2 out of 2 in 7g3k

Go back to Calcium Binding Sites List in 7g3k
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Chloro-4-[(7-Methyl-8-Oxo-5,6-Dihydroimidazo[1,5-A]Pyrazin-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C2N1CCN(C2=O)C)Cl)C#N with IC50=0.416172 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 5-Tert-Butyl-2- Chloro-4-[(7-Methyl-8-Oxo-5,6-Dihydroimidazo[1,5-A]Pyrazin-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C) OCC1=Nc=C2N1CCN(C2=O)C)Cl)C#N with IC50=0.416172 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1008

b:21.7
occ:1.00
 OD1 A:ASP171 1.9 22.7 1.0
OG1 A:THR209 2.0 21.2 1.0
NE2 A:HIS359 2.1 15.4 1.0
OD2 A:ASP358 2.1 22.7 1.0
CG A:ASP171 2.6 20.8 1.0
OD2 A:ASP171 2.7 28.0 1.0
O A:ACT1004 2.7 44.8 1.0
CB A:THR209 3.0 18.7 1.0
CE1 A:HIS359 3.0 16.0 1.0
CG A:ASP358 3.1 20.9 1.0
CD2 A:HIS359 3.1 16.0 1.0
CG2 A:THR209 3.3 20.7 1.0
OD1 A:ASP358 3.4 18.4 1.0
CA A:THR209 3.4 17.0 1.0
C A:ACT1004 3.8 44.7 1.0
N A:THR209 3.9 16.6 1.0
CB A:ASP171 4.0 18.4 1.0
CH3 A:ACT1004 4.1 40.0 1.0
ND1 A:HIS359 4.1 15.0 1.0
OD1 A:ASP311 4.1 20.8 1.0
CG A:HIS359 4.2 14.2 1.0
O A:HOH1102 4.2 25.1 1.0
N A:GLY172 4.2 15.6 1.0
CA A:ASP171 4.3 18.3 1.0
CG A:ASP311 4.4 21.5 1.0
CB A:ASP358 4.4 17.6 1.0
CE1 A:HIS474 4.4 16.9 1.0
ZN A:ZN1005 4.5 19.5 1.0
NE2 A:HIS474 4.6 16.6 1.0
C A:ASP171 4.7 18.1 1.0
C A:LYS208 4.7 18.4 1.0
OD2 A:ASP311 4.8 25.8 1.0
CB A:ASP311 4.8 18.0 1.0
C A:THR209 4.8 16.7 1.0
OXT A:ACT1004 4.8 33.0 1.0
OH A:TYR306 5.0 24.8 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 22:21:17 2025

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