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Calcium in PDB 7g7t: Crystal Structure of Rat Autotaxin in Complex with 6-[(3AR,6AR)-5-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrole-2-Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C1(Ncc(CC1)S(=O)(=O)N)C(=O)N1C[C@@H]2[C@@H](C1)Cn(C2) C(=O)C1CC(Nc(C1)OCC1CCOCC1)C1CC1 with IC50=0.00465744 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 6-[(3AR,6AR)-5-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrole-2-Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C1(Ncc(CC1)S(=O)(=O)N)C(=O)N1C[C@@H]2[C@@H](C1)Cn(C2) C(=O)C1CC(Nc(C1)OCC1CCOCC1)C1CC1 with IC50=0.00465744 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 6-[(3AR,6AR)-5-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrole-2-Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C1(Ncc(CC1)S(=O)(=O)N)C(=O)N1C[C@@H]2[C@@H](C1)Cn(C2) C(=O)C1CC(Nc(C1)OCC1CCOCC1)C1CC1 with IC50=0.00465744 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 6-[(3AR,6AR)-5-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrole-2-Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C1(Ncc(CC1)S(=O)(=O)N)C(=O)N1C[C@@H]2[C@@H](C1)Cn(C2) C(=O)C1CC(Nc(C1)OCC1CCOCC1)C1CC1 with IC50=0.00465744 Microm, PDB code: 7g7t 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) 49.26 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.886, 92.516, 120.983, 90, 90, 90
R / Rfree (%) 19.5 / 22.8

Other elements in 7g7t:

The structure of Crystal Structure of Rat Autotaxin in Complex with 6-[(3AR,6AR)-5-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrole-2-Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C1(Ncc(CC1)S(=O)(=O)N)C(=O)N1C[C@@H]2[C@@H](C1)Cn(C2) C(=O)C1CC(Nc(C1)OCC1CCOCC1)C1CC1 with IC50=0.00465744 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 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 6-[(3AR,6AR)-5-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrole-2-Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C1(Ncc(CC1)S(=O)(=O)N)C(=O)N1C[C@@H]2[C@@H](C1)Cn(C2) C(=O)C1CC(Nc(C1)OCC1CCOCC1)C1CC1 with IC50=0.00465744 Microm (pdb code 7g7t). 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 6-[(3AR,6AR)-5-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrole-2-Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C1(Ncc(CC1)S(=O)(=O)N)C(=O)N1C[C@@H]2[C@@H](C1)Cn(C2) C(=O)C1CC(Nc(C1)OCC1CCOCC1)C1CC1 with IC50=0.00465744 Microm, PDB code: 7g7t:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g7t

Go back to Calcium Binding Sites List in 7g7t
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 6-[(3AR,6AR)-5-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrole-2-Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C1(Ncc(CC1)S(=O)(=O)N)C(=O)N1C[C@@H]2[C@@H](C1)Cn(C2) C(=O)C1CC(Nc(C1)OCC1CCOCC1)C1CC1 with IC50=0.00465744 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 6-[(3AR,6AR)-5-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrole-2-Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C1(Ncc(CC1)S(=O)(=O)N)C(=O)N1C[C@@H]2[C@@H](C1)Cn(C2) C(=O)C1CC(Nc(C1)OCC1CCOCC1)C1CC1 with IC50=0.00465744 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:37.9
occ:1.00
 OD1 A:ASP171 1.9 33.3 1.0
OG1 A:THR209 1.9 25.7 1.0
NE2 A:HIS359 2.1 25.7 1.0
OD2 A:ASP358 2.3 29.1 1.0
CG A:ASP171 2.7 30.7 1.0
CB A:THR209 2.9 26.3 1.0
OD2 A:ASP171 2.9 41.7 1.0
CE1 A:HIS359 2.9 26.4 1.0
CG2 A:THR209 3.1 25.6 1.0
CD2 A:HIS359 3.1 25.8 1.0
CG A:ASP358 3.1 26.1 1.0
OD1 A:ASP358 3.3 23.6 1.0
CA A:THR209 3.3 25.6 1.0
N A:THR209 4.0 26.2 1.0
O33 A:XVB901 4.0 48.0 1.0
CB A:ASP171 4.1 27.5 1.0
ND1 A:HIS359 4.1 25.6 1.0
OD1 A:ASP311 4.1 26.5 1.0
CG A:HIS359 4.2 25.5 1.0
N A:GLY172 4.2 24.9 1.0
CE1 A:HIS474 4.3 26.8 1.0
CA A:ASP171 4.4 25.3 1.0
CB A:ASP358 4.4 24.1 1.0
CG A:ASP311 4.5 27.0 1.0
ZN A:ZN905 4.5 28.5 1.0
NE2 A:HIS474 4.5 27.6 1.0
C3 A:XVB901 4.6 51.6 1.0
C A:THR209 4.6 25.1 1.0
C A:ASP171 4.7 26.6 1.0
C A:LYS208 4.8 28.3 1.0
CB A:ASP311 4.9 25.1 1.0
OD2 A:ASP311 4.9 29.5 1.0
O A:THR209 4.9 26.5 1.0
O A:HOH1001 5.0 36.8 1.0

Calcium binding site 2 out of 2 in 7g7t

Go back to Calcium Binding Sites List in 7g7t
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 6-[(3AR,6AR)-5-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrole-2-Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C1(Ncc(CC1)S(=O)(=O)N)C(=O)N1C[C@@H]2[C@@H](C1)Cn(C2) C(=O)C1CC(Nc(C1)OCC1CCOCC1)C1CC1 with IC50=0.00465744 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 6-[(3AR,6AR)-5-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrole-2-Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C1(Ncc(CC1)S(=O)(=O)N)C(=O)N1C[C@@H]2[C@@H](C1)Cn(C2) C(=O)C1CC(Nc(C1)OCC1CCOCC1)C1CC1 with IC50=0.00465744 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:25.3
occ:1.00
 OD1 A:ASP739 2.3 22.3 1.0
O A:LEU745 2.3 23.2 1.0
OD1 A:ASP747 2.3 24.6 1.0
O A:HOH1337 2.3 30.6 1.0
OD1 A:ASN741 2.3 27.6 1.0
OD1 A:ASP743 2.4 26.5 1.0
CG A:ASP743 3.4 27.1 1.0
CG A:ASN741 3.4 30.3 1.0
C A:LEU745 3.5 26.2 1.0
CG A:ASP739 3.5 23.1 1.0
CG A:ASP747 3.6 26.4 1.0
OD2 A:ASP743 3.8 27.2 1.0
ND2 A:ASN741 3.9 30.3 1.0
N A:ASP747 3.9 24.1 1.0
CA A:ASP739 4.0 22.5 1.0
C A:ARG746 4.1 25.3 1.0
N A:LEU745 4.1 24.6 1.0
CA A:ASP747 4.2 26.9 1.0
CA A:LEU745 4.2 23.8 1.0
O A:ARG746 4.2 25.3 1.0
CB A:ASP739 4.3 22.1 1.0
N A:ASP743 4.3 23.0 1.0
OD2 A:ASP747 4.4 24.7 1.0
O A:PHE738 4.4 22.9 1.0
OD2 A:ASP739 4.4 22.5 1.0
N A:ASN741 4.5 25.0 1.0
CB A:ASP747 4.5 23.7 1.0
C A:ASP739 4.5 24.7 1.0
N A:ARG746 4.5 23.4 1.0
CB A:LEU745 4.5 26.5 1.0
CB A:ASP743 4.6 24.1 1.0
OE2 A:GLU751 4.7 40.0 1.0
N A:TYR740 4.7 23.7 1.0
CB A:ASN741 4.7 26.9 1.0
CA A:ARG746 4.7 24.2 1.0
O A:HOH1349 4.8 47.0 1.0
CA A:ASP743 4.8 23.5 1.0
N A:TYR742 4.8 23.1 1.0
N A:GLY744 4.9 25.0 1.0
CA A:ASN741 4.9 25.1 1.0
C A:ASN741 4.9 27.0 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 16:05:08 2025

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