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Calcium in PDB 7g6c: Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Cyano-5-Methylphenoxy)Methyl]-5-Pyrrolidin-1-Yl-1,3-Oxazole-4- Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc(=C(O1)N1CCCC1) C#N)C)C#N with IC50=0.0607829 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Cyano-5-Methylphenoxy)Methyl]-5-Pyrrolidin-1-Yl-1,3-Oxazole-4- Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc(=C(O1)N1CCCC1) C#N)C)C#N with IC50=0.0607829 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Cyano-5-Methylphenoxy)Methyl]-5-Pyrrolidin-1-Yl-1,3-Oxazole-4- Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc(=C(O1)N1CCCC1) C#N)C)C#N with IC50=0.0607829 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Cyano-5-Methylphenoxy)Methyl]-5-Pyrrolidin-1-Yl-1,3-Oxazole-4- Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc(=C(O1)N1CCCC1) C#N)C)C#N with IC50=0.0607829 Microm, PDB code: 7g6c was solved by M.Stihle, J.Benz, D.Hunziker, T.Lubbers, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.68 / 2.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.73, 91.354, 119.293, 90, 90, 90
R / Rfree (%) 19.3 / 25.1

Other elements in 7g6c:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Cyano-5-Methylphenoxy)Methyl]-5-Pyrrolidin-1-Yl-1,3-Oxazole-4- Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc(=C(O1)N1CCCC1) C#N)C)C#N with IC50=0.0607829 Microm also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Cyano-5-Methylphenoxy)Methyl]-5-Pyrrolidin-1-Yl-1,3-Oxazole-4- Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc(=C(O1)N1CCCC1) C#N)C)C#N with IC50=0.0607829 Microm (pdb code 7g6c). 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-[(2-Tert-Butyl-4- Cyano-5-Methylphenoxy)Methyl]-5-Pyrrolidin-1-Yl-1,3-Oxazole-4- Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc(=C(O1)N1CCCC1) C#N)C)C#N with IC50=0.0607829 Microm, PDB code: 7g6c:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g6c

Go back to Calcium Binding Sites List in 7g6c
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Cyano-5-Methylphenoxy)Methyl]-5-Pyrrolidin-1-Yl-1,3-Oxazole-4- Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc(=C(O1)N1CCCC1) C#N)C)C#N with IC50=0.0607829 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-[(2-Tert-Butyl-4- Cyano-5-Methylphenoxy)Methyl]-5-Pyrrolidin-1-Yl-1,3-Oxazole-4- Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc(=C(O1)N1CCCC1) C#N)C)C#N with IC50=0.0607829 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:50.3
occ:1.00
 OG1 A:THR209 1.7 37.7 1.0
OD1 A:ASP171 1.9 37.7 1.0
NE2 A:HIS359 2.1 31.2 1.0
OD2 A:ASP358 2.5 38.1 1.0
CG A:ASP171 2.6 37.1 1.0
OD2 A:ASP171 2.7 40.2 1.0
CB A:THR209 2.9 33.6 1.0
CE1 A:HIS359 3.0 30.3 1.0
O A:HOH1104 3.1 33.1 1.0
CD2 A:HIS359 3.2 30.0 1.0
CG2 A:THR209 3.3 33.2 1.0
CG A:ASP358 3.4 35.1 1.0
CA A:THR209 3.6 33.2 1.0
OD1 A:ASP358 3.7 36.6 1.0
CB A:ASP171 4.0 34.0 1.0
N A:THR209 4.0 34.3 1.0
OD1 A:ASP311 4.0 29.5 1.0
CE1 A:HIS474 4.1 30.7 1.0
ND1 A:HIS359 4.1 29.9 1.0
CG A:ASP311 4.2 32.2 1.0
O A:HOH1001 4.2 41.8 1.0
ZN A:ZN903 4.2 34.2 1.0
CG A:HIS359 4.2 30.2 1.0
NE2 A:HIS474 4.4 30.2 1.0
N A:GLY172 4.4 32.6 1.0
CA A:ASP171 4.4 32.6 1.0
OD2 A:ASP311 4.5 34.5 1.0
CB A:ASP311 4.5 32.7 1.0
OH A:TYR306 4.7 38.8 1.0
C A:LYS208 4.7 35.4 1.0
CB A:ASP358 4.7 33.9 1.0
C A:ASP171 4.8 33.6 1.0
O A:HOH1218 4.8 45.1 1.0
C A:THR209 4.9 32.9 1.0
ND1 A:HIS474 4.9 30.4 1.0

Calcium binding site 2 out of 2 in 7g6c

Go back to Calcium Binding Sites List in 7g6c
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Cyano-5-Methylphenoxy)Methyl]-5-Pyrrolidin-1-Yl-1,3-Oxazole-4- Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc(=C(O1)N1CCCC1) C#N)C)C#N with IC50=0.0607829 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-[(2-Tert-Butyl-4- Cyano-5-Methylphenoxy)Methyl]-5-Pyrrolidin-1-Yl-1,3-Oxazole-4- Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc(=C(O1)N1CCCC1) C#N)C)C#N with IC50=0.0607829 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:34.0
occ:1.00
 OD1 A:ASP747 2.2 31.4 1.0
O A:LEU745 2.2 31.5 1.0
O A:HOH1206 2.2 42.1 1.0
OD1 A:ASN741 2.2 35.4 1.0
OD1 A:ASP739 2.4 35.8 1.0
OD1 A:ASP743 2.4 27.3 1.0
CG A:ASN741 3.3 33.9 1.0
CG A:ASP743 3.4 28.7 1.0
C A:LEU745 3.4 31.3 1.0
CG A:ASP747 3.4 31.2 1.0
CG A:ASP739 3.5 33.2 1.0
ND2 A:ASN741 3.6 33.3 1.0
OD2 A:ASP743 3.7 28.6 1.0
N A:ASP747 3.8 31.9 1.0
CA A:ASP739 3.9 30.4 1.0
C A:ARG746 4.0 32.0 1.0
CA A:ASP747 4.1 33.0 1.0
N A:LEU745 4.1 29.6 1.0
CB A:ASP739 4.1 31.1 1.0
CA A:LEU745 4.2 29.9 1.0
OD2 A:ASP747 4.2 29.3 1.0
O A:ARG746 4.3 31.2 1.0
O A:PHE738 4.3 26.3 1.0
CB A:ASP747 4.3 32.0 1.0
OD2 A:ASP739 4.4 31.8 1.0
N A:ASP743 4.4 31.5 1.0
C A:ASP739 4.4 31.0 1.0
N A:ARG746 4.4 31.8 1.0
N A:ASN741 4.5 31.7 1.0
CB A:LEU745 4.5 29.8 1.0
CB A:ASN741 4.6 30.6 1.0
CA A:ARG746 4.7 31.5 1.0
CB A:ASP743 4.7 29.2 1.0
N A:TYR742 4.7 33.7 1.0
N A:TYR740 4.7 29.8 1.0
OE2 A:GLU751 4.8 42.7 1.0
C A:ASN741 4.8 33.7 1.0
CA A:ASN741 4.8 32.1 1.0
N A:ASP739 4.9 29.6 1.0
CA A:ASP743 4.9 29.1 1.0
N A:GLY744 5.0 29.9 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 15:55:17 2025

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