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Calcium in PDB 7g2r: Crystal Structure of Rat Autotaxin in Complex with 7-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]-2,5,6,8-Tetrahydro-[1,2, 4]Triazolo[4,3-A]Pyrazin-3-One, I.E. Smiles N1(C(=O)N2CC3=C(C2) Cn(C3)C(=O)C2CC(OCC3CCOCC3)Nc(C3CC3)C2)CC2=Nnc(=O)N2CC1 with IC50=0.00627428 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 7-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]-2,5,6,8-Tetrahydro-[1,2, 4]Triazolo[4,3-A]Pyrazin-3-One, I.E. Smiles N1(C(=O)N2CC3=C(C2) Cn(C3)C(=O)C2CC(OCC3CCOCC3)Nc(C3CC3)C2)CC2=Nnc(=O)N2CC1 with IC50=0.00627428 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 7-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]-2,5,6,8-Tetrahydro-[1,2, 4]Triazolo[4,3-A]Pyrazin-3-One, I.E. Smiles N1(C(=O)N2CC3=C(C2) Cn(C3)C(=O)C2CC(OCC3CCOCC3)Nc(C3CC3)C2)CC2=Nnc(=O)N2CC1 with IC50=0.00627428 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 7-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]-2,5,6,8-Tetrahydro-[1,2, 4]Triazolo[4,3-A]Pyrazin-3-One, I.E. Smiles N1(C(=O)N2CC3=C(C2) Cn(C3)C(=O)C2CC(OCC3CCOCC3)Nc(C3CC3)C2)CC2=Nnc(=O)N2CC1 with IC50=0.00627428 Microm, PDB code: 7g2r 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) 43.23 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.185, 91.866, 120.483, 90, 90, 90
R / Rfree (%) 17.8 / 20.5

Other elements in 7g2r:

The structure of Crystal Structure of Rat Autotaxin in Complex with 7-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]-2,5,6,8-Tetrahydro-[1,2, 4]Triazolo[4,3-A]Pyrazin-3-One, I.E. Smiles N1(C(=O)N2CC3=C(C2) Cn(C3)C(=O)C2CC(OCC3CCOCC3)Nc(C3CC3)C2)CC2=Nnc(=O)N2CC1 with IC50=0.00627428 Microm also contains other interesting chemical elements:

Potassium (K) 1 atom
Chlorine (Cl) 1 atom
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 7-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]-2,5,6,8-Tetrahydro-[1,2, 4]Triazolo[4,3-A]Pyrazin-3-One, I.E. Smiles N1(C(=O)N2CC3=C(C2) Cn(C3)C(=O)C2CC(OCC3CCOCC3)Nc(C3CC3)C2)CC2=Nnc(=O)N2CC1 with IC50=0.00627428 Microm (pdb code 7g2r). 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 7-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]-2,5,6,8-Tetrahydro-[1,2, 4]Triazolo[4,3-A]Pyrazin-3-One, I.E. Smiles N1(C(=O)N2CC3=C(C2) Cn(C3)C(=O)C2CC(OCC3CCOCC3)Nc(C3CC3)C2)CC2=Nnc(=O)N2CC1 with IC50=0.00627428 Microm, PDB code: 7g2r:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g2r

Go back to Calcium Binding Sites List in 7g2r
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 7-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]-2,5,6,8-Tetrahydro-[1,2, 4]Triazolo[4,3-A]Pyrazin-3-One, I.E. Smiles N1(C(=O)N2CC3=C(C2) Cn(C3)C(=O)C2CC(OCC3CCOCC3)Nc(C3CC3)C2)CC2=Nnc(=O)N2CC1 with IC50=0.00627428 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 7-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]-2,5,6,8-Tetrahydro-[1,2, 4]Triazolo[4,3-A]Pyrazin-3-One, I.E. Smiles N1(C(=O)N2CC3=C(C2) Cn(C3)C(=O)C2CC(OCC3CCOCC3)Nc(C3CC3)C2)CC2=Nnc(=O)N2CC1 with IC50=0.00627428 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:37.1
occ:1.00
 OD1 A:ASP171 1.7 22.3 1.0
OG1 A:THR209 1.9 20.4 1.0
NE2 A:HIS359 2.1 16.5 1.0
OD2 A:ASP358 2.3 18.3 1.0
CG A:ASP171 2.7 21.7 1.0
CB A:THR209 2.9 18.5 1.0
CE1 A:HIS359 2.9 16.3 1.0
CG A:ASP358 3.0 16.5 1.0
CD2 A:HIS359 3.1 15.7 1.0
CG2 A:THR209 3.1 21.2 1.0
OD2 A:ASP171 3.3 24.6 1.0
OD1 A:ASP358 3.3 15.3 1.0
CA A:THR209 3.4 18.1 1.0
CB A:ASP171 3.9 18.6 1.0
N A:THR209 3.9 17.2 1.0
ND1 A:HIS359 4.0 16.4 1.0
N38 A:XSU902 4.0 35.0 1.0
CG A:HIS359 4.1 14.6 1.0
OD2 A:ASP311 4.2 18.9 1.0
N A:GLY172 4.2 16.9 1.0
CA A:ASP171 4.2 18.4 1.0
O A:HOH1011 4.2 33.1 1.0
CB A:ASP358 4.3 15.3 1.0
CE1 A:HIS474 4.4 18.4 1.0
N37 A:XSU902 4.4 26.8 1.0
C A:ASP171 4.6 17.3 1.0
ZN A:ZN906 4.6 18.0 1.0
C A:THR209 4.6 17.6 1.0
NE2 A:HIS474 4.6 18.4 1.0
CG A:ASP311 4.6 17.4 1.0
C32 A:XSU902 4.7 33.3 1.0
C A:LYS208 4.7 17.8 1.0
OH A:TYR306 4.9 21.7 1.0
CB A:ASP311 5.0 17.6 1.0

Calcium binding site 2 out of 2 in 7g2r

Go back to Calcium Binding Sites List in 7g2r
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 7-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]-2,5,6,8-Tetrahydro-[1,2, 4]Triazolo[4,3-A]Pyrazin-3-One, I.E. Smiles N1(C(=O)N2CC3=C(C2) Cn(C3)C(=O)C2CC(OCC3CCOCC3)Nc(C3CC3)C2)CC2=Nnc(=O)N2CC1 with IC50=0.00627428 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 7-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]-2,5,6,8-Tetrahydro-[1,2, 4]Triazolo[4,3-A]Pyrazin-3-One, I.E. Smiles N1(C(=O)N2CC3=C(C2) Cn(C3)C(=O)C2CC(OCC3CCOCC3)Nc(C3CC3)C2)CC2=Nnc(=O)N2CC1 with IC50=0.00627428 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:16.1
occ:1.00
 OD1 A:ASP747 2.3 17.2 1.0
OD1 A:ASP739 2.3 15.9 1.0
OD1 A:ASN741 2.3 18.9 1.0
O A:HOH1384 2.3 20.8 1.0
O A:LEU745 2.3 16.6 1.0
OD1 A:ASP743 2.3 17.5 1.0
CG A:ASP743 3.3 17.1 1.0
CG A:ASN741 3.4 20.5 1.0
C A:LEU745 3.5 16.6 1.0
CG A:ASP739 3.5 16.0 1.0
CG A:ASP747 3.5 15.3 1.0
OD2 A:ASP743 3.7 18.6 1.0
ND2 A:ASN741 3.8 21.6 1.0
N A:ASP747 3.9 14.7 1.0
CA A:ASP739 4.0 14.9 1.0
C A:ARG746 4.0 16.5 1.0
N A:LEU745 4.1 15.3 1.0
CA A:ASP747 4.1 15.5 1.0
O A:ARG746 4.2 16.1 1.0
CA A:LEU745 4.2 15.8 1.0
CB A:ASP739 4.2 16.2 1.0
N A:ASP743 4.3 16.2 1.0
OD2 A:ASP739 4.4 15.7 1.0
OD2 A:ASP747 4.4 15.8 1.0
CB A:ASP747 4.4 15.2 1.0
O A:PHE738 4.4 14.3 1.0
CB A:LEU745 4.4 16.1 1.0
N A:ARG746 4.5 15.9 1.0
N A:ASN741 4.5 17.9 1.0
CB A:ASP743 4.5 17.1 1.0
C A:ASP739 4.5 16.0 1.0
OE2 A:GLU751 4.5 27.8 1.0
O A:HOH1303 4.7 26.2 1.0
CB A:ASN741 4.7 19.4 1.0
N A:TYR742 4.7 17.7 1.0
CA A:ARG746 4.7 16.5 1.0
N A:TYR740 4.8 17.2 1.0
CA A:ASP743 4.8 15.9 1.0
C A:ASN741 4.8 18.7 1.0
N A:GLY744 4.9 15.2 1.0
CA A:ASN741 4.9 17.9 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 15:35:09 2025

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