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Calcium in PDB 7g3m: Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methyl-N-(Oxetan-3-Yl)Imidazole-4- Carboxamide, I.E. Smiles CLC1C(C#N)Cc(C(C)(C)C)C(C1)OCC1=Nc=C(C(=O) NC2COC2)N1C with IC50=0.0161695 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methyl-N-(Oxetan-3-Yl)Imidazole-4- Carboxamide, I.E. Smiles CLC1C(C#N)Cc(C(C)(C)C)C(C1)OCC1=Nc=C(C(=O) NC2COC2)N1C with IC50=0.0161695 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methyl-N-(Oxetan-3-Yl)Imidazole-4- Carboxamide, I.E. Smiles CLC1C(C#N)Cc(C(C)(C)C)C(C1)OCC1=Nc=C(C(=O) NC2COC2)N1C with IC50=0.0161695 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methyl-N-(Oxetan-3-Yl)Imidazole-4- Carboxamide, I.E. Smiles CLC1C(C#N)Cc(C(C)(C)C)C(C1)OCC1=Nc=C(C(=O) NC2COC2)N1C with IC50=0.0161695 Microm, PDB code: 7g3m 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) 69.08 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.124, 91.755, 120.511, 90, 90, 90
R / Rfree (%) 17.5 / 22.4

Other elements in 7g3m:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methyl-N-(Oxetan-3-Yl)Imidazole-4- Carboxamide, I.E. Smiles CLC1C(C#N)Cc(C(C)(C)C)C(C1)OCC1=Nc=C(C(=O) NC2COC2)N1C with IC50=0.0161695 Microm also contains other interesting chemical elements:

Sodium (Na) 1 atom
Potassium (K) 1 atom
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-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methyl-N-(Oxetan-3-Yl)Imidazole-4- Carboxamide, I.E. Smiles CLC1C(C#N)Cc(C(C)(C)C)C(C1)OCC1=Nc=C(C(=O) NC2COC2)N1C with IC50=0.0161695 Microm (pdb code 7g3m). 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-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methyl-N-(Oxetan-3-Yl)Imidazole-4- Carboxamide, I.E. Smiles CLC1C(C#N)Cc(C(C)(C)C)C(C1)OCC1=Nc=C(C(=O) NC2COC2)N1C with IC50=0.0161695 Microm, PDB code: 7g3m:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g3m

Go back to Calcium Binding Sites List in 7g3m
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methyl-N-(Oxetan-3-Yl)Imidazole-4- Carboxamide, I.E. Smiles CLC1C(C#N)Cc(C(C)(C)C)C(C1)OCC1=Nc=C(C(=O) NC2COC2)N1C with IC50=0.0161695 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-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methyl-N-(Oxetan-3-Yl)Imidazole-4- Carboxamide, I.E. Smiles CLC1C(C#N)Cc(C(C)(C)C)C(C1)OCC1=Nc=C(C(=O) NC2COC2)N1C with IC50=0.0161695 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:25.2
occ:1.00
 OG1 A:THR209 1.8 20.2 1.0
OD1 A:ASP171 1.9 24.1 1.0
NE2 A:HIS359 2.1 18.2 1.0
O A:ACT907 2.3 38.8 1.0
OD2 A:ASP358 2.4 24.6 1.0
CG A:ASP171 2.6 21.2 1.0
OD2 A:ASP171 2.6 29.7 1.0
CE1 A:HIS359 3.0 19.2 1.0
CB A:THR209 3.1 22.0 1.0
CD2 A:HIS359 3.1 19.1 1.0
CG A:ASP358 3.2 23.3 1.0
C A:ACT907 3.4 46.0 1.0
CG2 A:THR209 3.5 25.9 1.0
OD1 A:ASP358 3.5 17.5 1.0
CA A:THR209 3.5 20.2 1.0
CH3 A:ACT907 3.8 41.7 1.0
N A:THR209 3.9 19.5 1.0
CB A:ASP171 4.0 18.7 1.0
O A:HOH1001 4.0 22.0 1.0
ND1 A:HIS359 4.1 16.3 1.0
OD1 A:ASP311 4.1 22.6 1.0
CG A:HIS359 4.2 16.8 1.0
CE1 A:HIS474 4.3 19.1 1.0
CG A:ASP311 4.3 21.4 1.0
CA A:ASP171 4.4 19.3 1.0
ZN A:ZN901 4.4 22.0 1.0
N A:GLY172 4.4 18.9 1.0
OXT A:ACT907 4.4 28.3 1.0
NE2 A:HIS474 4.4 18.7 1.0
CB A:ASP358 4.6 19.9 1.0
OD2 A:ASP311 4.6 27.0 1.0
CB A:ASP311 4.7 22.4 1.0
C A:LYS208 4.7 19.9 1.0
C A:ASP171 4.7 18.3 1.0
C A:THR209 4.9 18.8 1.0
OH A:TYR306 5.0 27.7 1.0

Calcium binding site 2 out of 2 in 7g3m

Go back to Calcium Binding Sites List in 7g3m
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methyl-N-(Oxetan-3-Yl)Imidazole-4- Carboxamide, I.E. Smiles CLC1C(C#N)Cc(C(C)(C)C)C(C1)OCC1=Nc=C(C(=O) NC2COC2)N1C with IC50=0.0161695 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-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methyl-N-(Oxetan-3-Yl)Imidazole-4- Carboxamide, I.E. Smiles CLC1C(C#N)Cc(C(C)(C)C)C(C1)OCC1=Nc=C(C(=O) NC2COC2)N1C with IC50=0.0161695 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:18.2
occ:1.00
 OD1 A:ASP739 2.3 16.9 1.0
OD1 A:ASP747 2.3 20.3 1.0
OD1 A:ASP743 2.3 18.6 1.0
O A:HOH1411 2.3 21.0 1.0
OD1 A:ASN741 2.3 20.8 1.0
O A:LEU745 2.3 18.1 1.0
CG A:ASP743 3.3 21.3 1.0
CG A:ASN741 3.4 23.5 1.0
CG A:ASP739 3.4 16.4 1.0
C A:LEU745 3.5 17.7 1.0
CG A:ASP747 3.6 20.1 1.0
OD2 A:ASP743 3.7 22.6 1.0
ND2 A:ASN741 3.8 20.3 1.0
CA A:ASP739 3.9 14.8 1.0
N A:ASP747 3.9 15.9 1.0
C A:ARG746 4.1 17.5 1.0
N A:LEU745 4.1 16.3 1.0
CB A:ASP739 4.2 15.4 1.0
CA A:ASP747 4.2 16.8 1.0
CA A:LEU745 4.2 16.4 1.0
O A:ARG746 4.3 17.0 1.0
N A:ASP743 4.3 17.9 1.0
OD2 A:ASP739 4.4 16.1 1.0
OD2 A:ASP747 4.4 19.6 1.0
CB A:LEU745 4.4 19.4 1.0
CB A:ASP747 4.4 17.7 1.0
O A:PHE738 4.4 15.4 1.0
CB A:ASP743 4.5 18.5 1.0
N A:ASN741 4.5 19.7 1.0
N A:ARG746 4.5 18.5 1.0
C A:ASP739 4.5 19.1 1.0
O A:HOH1353 4.5 35.2 1.0
OE2 A:GLU751 4.6 37.0 1.0
N A:TYR740 4.7 19.9 1.0
CB A:ASN741 4.7 20.8 1.0
CA A:ARG746 4.8 18.3 1.0
N A:TYR742 4.8 18.6 1.0
CA A:ASP743 4.8 18.6 1.0
N A:GLY744 4.8 16.3 1.0
C A:ASN741 4.9 21.7 1.0
CA A:ASN741 5.0 21.4 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 15:38:32 2025

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