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Calcium in PDB 7g7u: Crystal Structure of Rat Autotaxin in Complex with 4-[(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]-3- Fluorobenzenesulfonamide, I.E. Smiles C1(Ccc(CC1F)S(=O)(=O)N)C(=O) N1C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)C1CC1 with IC50=0.00563561 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[(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]-3- Fluorobenzenesulfonamide, I.E. Smiles C1(Ccc(CC1F)S(=O)(=O)N)C(=O) N1C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)C1CC1 with IC50=0.00563561 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[(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]-3- Fluorobenzenesulfonamide, I.E. Smiles C1(Ccc(CC1F)S(=O)(=O)N)C(=O) N1C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)C1CC1 with IC50=0.00563561 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[(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]-3- Fluorobenzenesulfonamide, I.E. Smiles C1(Ccc(CC1F)S(=O)(=O)N)C(=O) N1C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)C1CC1 with IC50=0.00563561 Microm, PDB code: 7g7u 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) 45.65 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.267, 91.308, 117.604, 90, 90, 90
R / Rfree (%) 19.4 / 23.5

Other elements in 7g7u:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[(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]-3- Fluorobenzenesulfonamide, I.E. Smiles C1(Ccc(CC1F)S(=O)(=O)N)C(=O) N1C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)C1CC1 with IC50=0.00563561 Microm also contains other interesting chemical elements:

Potassium (K) 1 atom
Zinc (Zn) 1 atom
Sodium (Na) 1 atom
Fluorine (F) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 4-[(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]-3- Fluorobenzenesulfonamide, I.E. Smiles C1(Ccc(CC1F)S(=O)(=O)N)C(=O) N1C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)C1CC1 with IC50=0.00563561 Microm (pdb code 7g7u). 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 4-[(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]-3- Fluorobenzenesulfonamide, I.E. Smiles C1(Ccc(CC1F)S(=O)(=O)N)C(=O) N1C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)C1CC1 with IC50=0.00563561 Microm, PDB code: 7g7u:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g7u

Go back to Calcium Binding Sites List in 7g7u
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-[(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]-3- Fluorobenzenesulfonamide, I.E. Smiles C1(Ccc(CC1F)S(=O)(=O)N)C(=O) N1C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)C1CC1 with IC50=0.00563561 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 4-[(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]-3- Fluorobenzenesulfonamide, I.E. Smiles C1(Ccc(CC1F)S(=O)(=O)N)C(=O) N1C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)C1CC1 with IC50=0.00563561 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:45.5
occ:1.00
 OD1 A:ASP171 1.8 39.4 1.0
OG1 A:THR209 1.9 27.6 1.0
NE2 A:HIS359 2.2 30.3 1.0
OD2 A:ASP358 2.3 33.5 1.0
CG A:ASP171 2.7 37.0 1.0
CB A:THR209 2.8 28.7 1.0
OD2 A:ASP171 3.0 47.4 1.0
CG2 A:THR209 3.0 30.2 1.0
CG A:ASP358 3.2 32.6 1.0
CD2 A:HIS359 3.2 27.3 1.0
CE1 A:HIS359 3.2 30.3 1.0
CA A:THR209 3.3 27.0 1.0
OD1 A:ASP358 3.4 29.6 1.0
N A:THR209 3.9 27.7 1.0
N31 A:YE0901 3.9 60.1 1.0
CB A:ASP171 4.0 31.6 1.0
OD2 A:ASP311 4.2 25.0 1.0
ND1 A:HIS359 4.2 28.8 1.0
CG A:HIS359 4.3 28.1 1.0
N A:GLY172 4.3 27.2 1.0
CA A:ASP171 4.4 31.0 1.0
CB A:ASP358 4.4 27.6 1.0
CE1 A:HIS474 4.4 23.1 1.0
C A:THR209 4.5 26.1 1.0
CG A:ASP311 4.5 30.5 1.0
ZN A:ZN905 4.6 33.8 1.0
C5 A:YE0901 4.7 57.6 1.0
C A:ASP171 4.7 29.1 1.0
C A:LYS208 4.8 31.6 1.0
NE2 A:HIS474 4.8 26.2 1.0
O A:THR209 4.8 24.6 1.0
OH A:TYR306 4.9 42.9 1.0
S30 A:YE0901 4.9 51.9 1.0
CB A:ASP311 4.9 26.2 1.0
O33 A:YE0901 5.0 60.7 1.0
OD1 A:ASP311 5.0 32.5 1.0

Calcium binding site 2 out of 2 in 7g7u

Go back to Calcium Binding Sites List in 7g7u
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-[(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]-3- Fluorobenzenesulfonamide, I.E. Smiles C1(Ccc(CC1F)S(=O)(=O)N)C(=O) N1C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)C1CC1 with IC50=0.00563561 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 4-[(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]-3- Fluorobenzenesulfonamide, I.E. Smiles C1(Ccc(CC1F)S(=O)(=O)N)C(=O) N1C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)C1CC1 with IC50=0.00563561 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:28.5
occ:1.00
 OD1 A:ASP743 2.2 31.3 1.0
OD1 A:ASP739 2.3 25.5 1.0
O A:LEU745 2.3 24.8 1.0
OD1 A:ASP747 2.4 29.8 1.0
O A:HOH1176 2.4 32.9 1.0
OD1 A:ASN741 2.4 28.7 1.0
CG A:ASP743 3.2 32.0 1.0
CG A:ASN741 3.5 35.1 1.0
CG A:ASP739 3.5 25.8 1.0
C A:LEU745 3.5 31.9 1.0
OD2 A:ASP743 3.6 30.0 1.0
CG A:ASP747 3.6 29.9 1.0
ND2 A:ASN741 4.0 34.2 1.0
N A:ASP747 4.0 30.3 1.0
CA A:ASP739 4.1 28.2 1.0
N A:LEU745 4.1 27.4 1.0
C A:ARG746 4.1 29.7 1.0
O A:ARG746 4.2 28.2 1.0
CA A:LEU745 4.2 27.7 1.0
CA A:ASP747 4.2 31.4 1.0
CB A:ASP739 4.3 25.0 1.0
N A:ASP743 4.4 31.1 1.0
CB A:LEU745 4.4 28.6 1.0
OD2 A:ASP739 4.4 24.7 1.0
OD2 A:ASP747 4.4 31.2 1.0
O A:PHE738 4.5 28.4 1.0
CB A:ASP743 4.5 29.6 1.0
OE2 A:GLU751 4.5 44.8 1.0
C A:ASP739 4.5 29.4 1.0
CB A:ASP747 4.5 30.5 1.0
N A:ASN741 4.6 32.6 1.0
N A:ARG746 4.6 27.4 1.0
CA A:ASP743 4.8 30.2 1.0
N A:TYR740 4.8 26.9 1.0
CB A:ASN741 4.8 28.6 1.0
CA A:ARG746 4.8 29.2 1.0
N A:GLY744 4.8 29.5 1.0
N A:TYR742 4.9 31.1 1.0
C A:ASN741 4.9 32.4 1.0
CA A:ASN741 5.0 31.4 1.0
C A:ASP743 5.0 28.9 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: Wed Jul 9 22:39:51 2025

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