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Calcium in PDB 7g2u: Crystal Structure of Rat Autotaxin in Complex with [2-[2-Cyclopropyl- 6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3-Dihydroisoindol-5-Yl]- (3-Hydroxy-6,7-Dihydro-4H-[1,2]Oxazolo[4,5-C]Pyridin-5-Yl)Methanone, I.E. Smiles C1C(C1)C1CC(C(=O)N2CC3C(Ccc(C3)C(=O)N3CCC4=C(C3)C(=NO4) O)C2)Cc(OCC2CCOCC2)N1 with IC50=0.0102556 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [2-[2-Cyclopropyl- 6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3-Dihydroisoindol-5-Yl]- (3-Hydroxy-6,7-Dihydro-4H-[1,2]Oxazolo[4,5-C]Pyridin-5-Yl)Methanone, I.E. Smiles C1C(C1)C1CC(C(=O)N2CC3C(Ccc(C3)C(=O)N3CCC4=C(C3)C(=NO4) O)C2)Cc(OCC2CCOCC2)N1 with IC50=0.0102556 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [2-[2-Cyclopropyl- 6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3-Dihydroisoindol-5-Yl]- (3-Hydroxy-6,7-Dihydro-4H-[1,2]Oxazolo[4,5-C]Pyridin-5-Yl)Methanone, I.E. Smiles C1C(C1)C1CC(C(=O)N2CC3C(Ccc(C3)C(=O)N3CCC4=C(C3)C(=NO4) O)C2)Cc(OCC2CCOCC2)N1 with IC50=0.0102556 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [2-[2-Cyclopropyl- 6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3-Dihydroisoindol-5-Yl]- (3-Hydroxy-6,7-Dihydro-4H-[1,2]Oxazolo[4,5-C]Pyridin-5-Yl)Methanone, I.E. Smiles C1C(C1)C1CC(C(=O)N2CC3C(Ccc(C3)C(=O)N3CCC4=C(C3)C(=NO4) O)C2)Cc(OCC2CCOCC2)N1 with IC50=0.0102556 Microm, PDB code: 7g2u was solved by M.Stihle, J.Benz, D.Hunziker, P.Mattei, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.66 / 1.74
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.656, 90.916, 116.659, 90, 90, 90
R / Rfree (%) 18.1 / 22.2

Other elements in 7g2u:

The structure of Crystal Structure of Rat Autotaxin in Complex with [2-[2-Cyclopropyl- 6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3-Dihydroisoindol-5-Yl]- (3-Hydroxy-6,7-Dihydro-4H-[1,2]Oxazolo[4,5-C]Pyridin-5-Yl)Methanone, I.E. Smiles C1C(C1)C1CC(C(=O)N2CC3C(Ccc(C3)C(=O)N3CCC4=C(C3)C(=NO4) O)C2)Cc(OCC2CCOCC2)N1 with IC50=0.0102556 Microm also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom
Potassium (K) 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 [2-[2-Cyclopropyl- 6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3-Dihydroisoindol-5-Yl]- (3-Hydroxy-6,7-Dihydro-4H-[1,2]Oxazolo[4,5-C]Pyridin-5-Yl)Methanone, I.E. Smiles C1C(C1)C1CC(C(=O)N2CC3C(Ccc(C3)C(=O)N3CCC4=C(C3)C(=NO4) O)C2)Cc(OCC2CCOCC2)N1 with IC50=0.0102556 Microm (pdb code 7g2u). 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-Cyclopropyl- 6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3-Dihydroisoindol-5-Yl]- (3-Hydroxy-6,7-Dihydro-4H-[1,2]Oxazolo[4,5-C]Pyridin-5-Yl)Methanone, I.E. Smiles C1C(C1)C1CC(C(=O)N2CC3C(Ccc(C3)C(=O)N3CCC4=C(C3)C(=NO4) O)C2)Cc(OCC2CCOCC2)N1 with IC50=0.0102556 Microm, PDB code: 7g2u:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g2u

Go back to Calcium Binding Sites List in 7g2u
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [2-[2-Cyclopropyl- 6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3-Dihydroisoindol-5-Yl]- (3-Hydroxy-6,7-Dihydro-4H-[1,2]Oxazolo[4,5-C]Pyridin-5-Yl)Methanone, I.E. Smiles C1C(C1)C1CC(C(=O)N2CC3C(Ccc(C3)C(=O)N3CCC4=C(C3)C(=NO4) O)C2)Cc(OCC2CCOCC2)N1 with IC50=0.0102556 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-Cyclopropyl- 6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3-Dihydroisoindol-5-Yl]- (3-Hydroxy-6,7-Dihydro-4H-[1,2]Oxazolo[4,5-C]Pyridin-5-Yl)Methanone, I.E. Smiles C1C(C1)C1CC(C(=O)N2CC3C(Ccc(C3)C(=O)N3CCC4=C(C3)C(=NO4) O)C2)Cc(OCC2CCOCC2)N1 with IC50=0.0102556 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:22.1
occ:1.00
 OG1 A:THR209 1.7 25.2 1.0
OD1 A:ASP171 1.8 29.7 1.0
OD2 A:ASP358 2.1 24.2 1.0
NE2 A:HIS359 2.2 19.7 1.0
CG A:ASP171 2.5 24.4 1.0
OD2 A:ASP171 2.6 27.7 1.0
CB A:THR209 2.8 21.4 1.0
CG A:ASP358 3.0 23.6 1.0
CE1 A:HIS359 3.1 21.6 1.0
CD2 A:HIS359 3.1 20.4 1.0
CG2 A:THR209 3.2 23.9 1.0
O27 A:XVL904 3.2 30.3 1.0
CA A:THR209 3.3 19.0 1.0
OD1 A:ASP358 3.3 19.7 1.0
N A:THR209 3.9 19.6 1.0
C22 A:XVL904 3.9 31.4 1.0
CB A:ASP171 3.9 23.7 1.0
C21 A:XVL904 4.0 34.8 1.0
O A:HOH1052 4.2 24.5 1.0
ND1 A:HIS359 4.2 19.2 1.0
OD2 A:ASP311 4.2 21.7 1.0
CG A:HIS359 4.2 20.1 1.0
N A:GLY172 4.3 20.9 1.0
CB A:ASP358 4.4 21.0 1.0
CA A:ASP171 4.4 21.4 1.0
N26 A:XVL904 4.4 34.4 1.0
CE1 A:HIS474 4.5 19.6 1.0
CG A:ASP311 4.6 22.1 1.0
C A:THR209 4.6 18.6 1.0
C A:ASP171 4.7 21.7 1.0
ZN A:ZN906 4.7 23.6 1.0
C A:LYS208 4.7 22.0 1.0
OH A:TYR306 4.8 27.5 1.0
NE2 A:HIS474 4.9 17.6 1.0
CB A:ASP311 4.9 19.6 1.0

Calcium binding site 2 out of 2 in 7g2u

Go back to Calcium Binding Sites List in 7g2u
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [2-[2-Cyclopropyl- 6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3-Dihydroisoindol-5-Yl]- (3-Hydroxy-6,7-Dihydro-4H-[1,2]Oxazolo[4,5-C]Pyridin-5-Yl)Methanone, I.E. Smiles C1C(C1)C1CC(C(=O)N2CC3C(Ccc(C3)C(=O)N3CCC4=C(C3)C(=NO4) O)C2)Cc(OCC2CCOCC2)N1 with IC50=0.0102556 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-Cyclopropyl- 6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3-Dihydroisoindol-5-Yl]- (3-Hydroxy-6,7-Dihydro-4H-[1,2]Oxazolo[4,5-C]Pyridin-5-Yl)Methanone, I.E. Smiles C1C(C1)C1CC(C(=O)N2CC3C(Ccc(C3)C(=O)N3CCC4=C(C3)C(=NO4) O)C2)Cc(OCC2CCOCC2)N1 with IC50=0.0102556 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:19.7
occ:1.00
 OD1 A:ASP739 2.2 18.3 1.0
OD1 A:ASP743 2.2 18.0 1.0
OD1 A:ASP747 2.3 19.3 1.0
OD1 A:ASN741 2.3 21.1 1.0
O A:LEU745 2.4 18.7 1.0
O A:HOH1293 2.4 21.3 1.0
CG A:ASP743 3.2 19.8 1.0
CG A:ASN741 3.4 25.4 1.0
CG A:ASP739 3.4 18.1 1.0
CG A:ASP747 3.5 20.2 1.0
C A:LEU745 3.5 20.2 1.0
OD2 A:ASP743 3.6 22.1 1.0
ND2 A:ASN741 3.9 28.7 1.0
CA A:ASP739 3.9 18.6 1.0
N A:ASP747 4.0 20.1 1.0
C A:ARG746 4.1 22.2 1.0
N A:LEU745 4.1 18.6 1.0
CA A:ASP747 4.1 20.2 1.0
CB A:ASP739 4.2 18.5 1.0
O A:ARG746 4.2 17.8 1.0
CA A:LEU745 4.3 19.4 1.0
OD2 A:ASP739 4.3 18.8 1.0
N A:ASP743 4.4 20.4 1.0
OD2 A:ASP747 4.4 20.2 1.0
C A:ASP739 4.4 19.8 1.0
CB A:LEU745 4.4 20.3 1.0
CB A:ASP747 4.4 19.7 1.0
O A:PHE738 4.4 19.8 1.0
N A:ASN741 4.4 20.1 1.0
CB A:ASP743 4.5 20.3 1.0
N A:ARG746 4.5 20.0 1.0
CB A:ASN741 4.6 20.4 1.0
N A:TYR742 4.7 20.9 1.0
OE2 A:GLU751 4.7 31.7 1.0
N A:TYR740 4.7 18.9 1.0
C A:ASN741 4.8 20.2 1.0
CA A:ARG746 4.8 20.7 1.0
CA A:ASN741 4.8 19.5 1.0
CA A:ASP743 4.8 21.1 1.0
N A:GLY744 4.8 17.6 1.0
N A:ASP739 5.0 18.8 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: Sat Feb 8 15:35:08 2025

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