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Calcium in PDB 7g79: Crystal Structure of Rat Autotaxin in Complex with 1-[(3AS,6AS)-5-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-3-(1H-Triazol-5-Yl)Propan-1-One, I.E. Smiles N1(C(=O)C2CC(Nc(C2)C2CC2)OCC2CCOCC2)C[C@H]2[C@H](C1) Cn(C2)C(=O)CCC1=Cn=NN1 with IC50=0.250768 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1-[(3AS,6AS)-5-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-3-(1H-Triazol-5-Yl)Propan-1-One, I.E. Smiles N1(C(=O)C2CC(Nc(C2)C2CC2)OCC2CCOCC2)C[C@H]2[C@H](C1) Cn(C2)C(=O)CCC1=Cn=NN1 with IC50=0.250768 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1-[(3AS,6AS)-5-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-3-(1H-Triazol-5-Yl)Propan-1-One, I.E. Smiles N1(C(=O)C2CC(Nc(C2)C2CC2)OCC2CCOCC2)C[C@H]2[C@H](C1) Cn(C2)C(=O)CCC1=Cn=NN1 with IC50=0.250768 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 1-[(3AS,6AS)-5-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-3-(1H-Triazol-5-Yl)Propan-1-One, I.E. Smiles N1(C(=O)C2CC(Nc(C2)C2CC2)OCC2CCOCC2)C[C@H]2[C@H](C1) Cn(C2)C(=O)CCC1=Cn=NN1 with IC50=0.250768 Microm, PDB code: 7g79 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) 48.78 / 1.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.245, 91.757, 119.644, 90, 90, 90
R / Rfree (%) 18.4 / 21.4

Other elements in 7g79:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1-[(3AS,6AS)-5-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-3-(1H-Triazol-5-Yl)Propan-1-One, I.E. Smiles N1(C(=O)C2CC(Nc(C2)C2CC2)OCC2CCOCC2)C[C@H]2[C@H](C1) Cn(C2)C(=O)CCC1=Cn=NN1 with IC50=0.250768 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 1-[(3AS,6AS)-5-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-3-(1H-Triazol-5-Yl)Propan-1-One, I.E. Smiles N1(C(=O)C2CC(Nc(C2)C2CC2)OCC2CCOCC2)C[C@H]2[C@H](C1) Cn(C2)C(=O)CCC1=Cn=NN1 with IC50=0.250768 Microm (pdb code 7g79). 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 1-[(3AS,6AS)-5-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-3-(1H-Triazol-5-Yl)Propan-1-One, I.E. Smiles N1(C(=O)C2CC(Nc(C2)C2CC2)OCC2CCOCC2)C[C@H]2[C@H](C1) Cn(C2)C(=O)CCC1=Cn=NN1 with IC50=0.250768 Microm, PDB code: 7g79:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g79

Go back to Calcium Binding Sites List in 7g79
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1-[(3AS,6AS)-5-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-3-(1H-Triazol-5-Yl)Propan-1-One, I.E. Smiles N1(C(=O)C2CC(Nc(C2)C2CC2)OCC2CCOCC2)C[C@H]2[C@H](C1) Cn(C2)C(=O)CCC1=Cn=NN1 with IC50=0.250768 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 1-[(3AS,6AS)-5-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-3-(1H-Triazol-5-Yl)Propan-1-One, I.E. Smiles N1(C(=O)C2CC(Nc(C2)C2CC2)OCC2CCOCC2)C[C@H]2[C@H](C1) Cn(C2)C(=O)CCC1=Cn=NN1 with IC50=0.250768 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:18.3
occ:1.00
 O A:HOH1429 2.3 25.1 1.0
OD1 A:ASP747 2.3 21.3 1.0
O A:LEU745 2.3 17.5 1.0
OD1 A:ASN741 2.3 20.3 1.0
OD1 A:ASP739 2.3 19.0 1.0
OD1 A:ASP743 2.4 20.4 1.0
CG A:ASP743 3.3 21.0 1.0
CG A:ASN741 3.4 23.2 1.0
C A:LEU745 3.5 18.2 1.0
CG A:ASP739 3.5 18.6 1.0
CG A:ASP747 3.5 21.1 1.0
OD2 A:ASP743 3.8 22.8 1.0
ND2 A:ASN741 3.9 23.4 1.0
N A:ASP747 3.9 18.0 1.0
CA A:ASP739 4.0 16.8 1.0
N A:LEU745 4.0 18.1 1.0
C A:ARG746 4.0 18.6 1.0
CA A:ASP747 4.1 18.6 1.0
O A:ARG746 4.2 18.9 1.0
CA A:LEU745 4.2 17.6 1.0
CB A:ASP739 4.2 16.7 1.0
N A:ASP743 4.3 19.3 1.0
OD2 A:ASP747 4.4 19.7 1.0
CB A:ASP747 4.4 19.6 1.0
O A:PHE738 4.4 17.2 1.0
C A:ASP739 4.4 18.2 1.0
OD2 A:ASP739 4.4 19.2 1.0
N A:ASN741 4.5 19.5 1.0
CB A:LEU745 4.5 19.2 1.0
N A:ARG746 4.5 16.8 1.0
CB A:ASP743 4.6 19.8 1.0
OE2 A:GLU751 4.6 35.2 1.0
N A:TYR740 4.7 19.5 1.0
CB A:ASN741 4.7 21.6 1.0
CA A:ARG746 4.7 16.9 1.0
N A:TYR742 4.8 20.0 1.0
O A:HOH1410 4.8 33.1 1.0
CA A:ASP743 4.8 19.8 1.0
N A:GLY744 4.9 20.1 1.0
C A:ASN741 4.9 21.1 1.0
CA A:ASN741 4.9 21.0 1.0

Calcium binding site 2 out of 2 in 7g79

Go back to Calcium Binding Sites List in 7g79
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1-[(3AS,6AS)-5-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-3-(1H-Triazol-5-Yl)Propan-1-One, I.E. Smiles N1(C(=O)C2CC(Nc(C2)C2CC2)OCC2CCOCC2)C[C@H]2[C@H](C1) Cn(C2)C(=O)CCC1=Cn=NN1 with IC50=0.250768 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 1-[(3AS,6AS)-5-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-3-(1H-Triazol-5-Yl)Propan-1-One, I.E. Smiles N1(C(=O)C2CC(Nc(C2)C2CC2)OCC2CCOCC2)C[C@H]2[C@H](C1) Cn(C2)C(=O)CCC1=Cn=NN1 with IC50=0.250768 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:50.8
occ:1.00
 OD1 A:ASP171 1.9 27.6 1.0
OG1 A:THR209 2.1 33.4 1.0
NE2 A:HIS359 2.2 18.0 1.0
OD2 A:ASP358 2.3 21.0 1.0
CB A:THR209 2.9 26.9 1.0
CG A:ASP171 2.9 28.1 1.0
CG2 A:THR209 2.9 25.0 1.0
CE1 A:HIS359 3.0 18.5 1.0
CG A:ASP358 3.2 20.2 1.0
CD2 A:HIS359 3.2 18.9 1.0
CA A:THR209 3.3 22.1 1.0
OD2 A:ASP171 3.3 34.2 1.0
OD1 A:ASP358 3.5 19.4 1.0
N A:THR209 3.9 19.3 1.0
OD1 A:ASP311 4.1 22.0 1.0
ND1 A:HIS359 4.1 19.7 1.0
CB A:ASP171 4.1 21.0 1.0
C33 A:YB1901 4.2 54.4 1.0
CG A:HIS359 4.2 17.4 1.0
CE1 A:HIS474 4.3 20.4 1.0
N34 A:YB1901 4.3 42.9 1.0
N A:GLY172 4.3 17.4 1.0
CA A:ASP171 4.4 20.4 1.0
CB A:ASP358 4.4 18.7 1.0
O A:HOH1001 4.4 38.5 1.0
ZN A:ZN902 4.5 21.7 1.0
CG A:ASP311 4.5 20.6 1.0
C A:THR209 4.5 19.3 1.0
NE2 A:HIS474 4.5 20.4 1.0
C A:LYS208 4.7 20.5 1.0
C A:ASP171 4.7 19.3 1.0
O A:THR209 4.9 19.4 1.0
OD2 A:ASP311 4.9 24.2 1.0
OH A:TYR306 4.9 33.0 1.0
CB A:ASP311 4.9 18.3 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 22:37:18 2025

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