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Calcium in PDB 7g2x: Crystal Structure of Rat Autotaxin in Complex with 1-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-3,4,5,6- Tetrahydro-1H-Cyclopenta[C]Pyrrole-5-Carbonyl]Piperidine-4- Sulfonamide, I.E. Smiles C1C2=C(C[C@H]1C(=O)N1CC[C@@H](S(=O)(=O)N) CC1)Cn(C2)C(=O)C1CC(Nc(C1)C1CC1)OCC1CCOCC1 with IC50=0.0015731 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-3,4,5,6- Tetrahydro-1H-Cyclopenta[C]Pyrrole-5-Carbonyl]Piperidine-4- Sulfonamide, I.E. Smiles C1C2=C(C[C@H]1C(=O)N1CC[C@@H](S(=O)(=O)N) CC1)Cn(C2)C(=O)C1CC(Nc(C1)C1CC1)OCC1CCOCC1 with IC50=0.0015731 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-3,4,5,6- Tetrahydro-1H-Cyclopenta[C]Pyrrole-5-Carbonyl]Piperidine-4- Sulfonamide, I.E. Smiles C1C2=C(C[C@H]1C(=O)N1CC[C@@H](S(=O)(=O)N) CC1)Cn(C2)C(=O)C1CC(Nc(C1)C1CC1)OCC1CCOCC1 with IC50=0.0015731 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 1-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-3,4,5,6- Tetrahydro-1H-Cyclopenta[C]Pyrrole-5-Carbonyl]Piperidine-4- Sulfonamide, I.E. Smiles C1C2=C(C[C@H]1C(=O)N1CC[C@@H](S(=O)(=O)N) CC1)Cn(C2)C(=O)C1CC(Nc(C1)C1CC1)OCC1CCOCC1 with IC50=0.0015731 Microm, PDB code: 7g2x 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) 47.72 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.067, 90.832, 116.607, 90, 90, 90
R / Rfree (%) 17.1 / 20.2

Other elements in 7g2x:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-3,4,5,6- Tetrahydro-1H-Cyclopenta[C]Pyrrole-5-Carbonyl]Piperidine-4- Sulfonamide, I.E. Smiles C1C2=C(C[C@H]1C(=O)N1CC[C@@H](S(=O)(=O)N) CC1)Cn(C2)C(=O)C1CC(Nc(C1)C1CC1)OCC1CCOCC1 with IC50=0.0015731 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-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-3,4,5,6- Tetrahydro-1H-Cyclopenta[C]Pyrrole-5-Carbonyl]Piperidine-4- Sulfonamide, I.E. Smiles C1C2=C(C[C@H]1C(=O)N1CC[C@@H](S(=O)(=O)N) CC1)Cn(C2)C(=O)C1CC(Nc(C1)C1CC1)OCC1CCOCC1 with IC50=0.0015731 Microm (pdb code 7g2x). 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-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-3,4,5,6- Tetrahydro-1H-Cyclopenta[C]Pyrrole-5-Carbonyl]Piperidine-4- Sulfonamide, I.E. Smiles C1C2=C(C[C@H]1C(=O)N1CC[C@@H](S(=O)(=O)N) CC1)Cn(C2)C(=O)C1CC(Nc(C1)C1CC1)OCC1CCOCC1 with IC50=0.0015731 Microm, PDB code: 7g2x:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g2x

Go back to Calcium Binding Sites List in 7g2x
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-3,4,5,6- Tetrahydro-1H-Cyclopenta[C]Pyrrole-5-Carbonyl]Piperidine-4- Sulfonamide, I.E. Smiles C1C2=C(C[C@H]1C(=O)N1CC[C@@H](S(=O)(=O)N) CC1)Cn(C2)C(=O)C1CC(Nc(C1)C1CC1)OCC1CCOCC1 with IC50=0.0015731 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-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-3,4,5,6- Tetrahydro-1H-Cyclopenta[C]Pyrrole-5-Carbonyl]Piperidine-4- Sulfonamide, I.E. Smiles C1C2=C(C[C@H]1C(=O)N1CC[C@@H](S(=O)(=O)N) CC1)Cn(C2)C(=O)C1CC(Nc(C1)C1CC1)OCC1CCOCC1 with IC50=0.0015731 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:23.2
occ:1.00
 OD1 A:ASP171 1.8 24.4 1.0
OG1 A:THR209 1.9 21.1 1.0
NE2 A:HIS359 2.1 18.7 1.0
OD2 A:ASP358 2.1 19.9 1.0
CG A:ASP171 2.6 24.0 1.0
OD2 A:ASP171 2.9 35.6 1.0
CB A:THR209 2.9 21.5 1.0
CE1 A:HIS359 2.9 18.6 1.0
CG A:ASP358 3.0 19.5 1.0
CD2 A:HIS359 3.1 19.0 1.0
CG2 A:THR209 3.2 21.6 1.0
OD1 A:ASP358 3.3 17.4 1.0
CA A:THR209 3.4 17.7 1.0
N14 A:XFO906 3.9 31.9 1.0
CB A:ASP171 4.0 19.1 1.0
OD1 A:ASP311 4.0 19.9 1.0
ND1 A:HIS359 4.0 18.4 1.0
N A:THR209 4.0 18.1 1.0
CG A:HIS359 4.1 17.2 1.0
N A:GLY172 4.2 16.9 1.0
CB A:ASP358 4.3 17.1 1.0
CE1 A:HIS474 4.3 19.4 1.0
CA A:ASP171 4.3 18.4 1.0
CG A:ASP311 4.4 19.6 1.0
C9 A:XFO906 4.4 30.3 1.0
ZN A:ZN909 4.4 20.0 1.0
NE2 A:HIS474 4.6 20.0 1.0
C A:ASP171 4.6 19.2 1.0
C A:THR209 4.7 17.0 1.0
CB A:ASP311 4.8 18.2 1.0
C A:LYS208 4.8 18.4 1.0
O A:HOH1002 4.8 30.6 1.0
OD2 A:ASP311 4.9 21.3 1.0
CA A:GLY172 4.9 17.7 1.0
O A:THR209 5.0 16.0 1.0

Calcium binding site 2 out of 2 in 7g2x

Go back to Calcium Binding Sites List in 7g2x
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-3,4,5,6- Tetrahydro-1H-Cyclopenta[C]Pyrrole-5-Carbonyl]Piperidine-4- Sulfonamide, I.E. Smiles C1C2=C(C[C@H]1C(=O)N1CC[C@@H](S(=O)(=O)N) CC1)Cn(C2)C(=O)C1CC(Nc(C1)C1CC1)OCC1CCOCC1 with IC50=0.0015731 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-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-3,4,5,6- Tetrahydro-1H-Cyclopenta[C]Pyrrole-5-Carbonyl]Piperidine-4- Sulfonamide, I.E. Smiles C1C2=C(C[C@H]1C(=O)N1CC[C@@H](S(=O)(=O)N) CC1)Cn(C2)C(=O)C1CC(Nc(C1)C1CC1)OCC1CCOCC1 with IC50=0.0015731 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca911

b:17.3
occ:1.00
 OD1 A:ASP747 2.3 18.4 1.0
OD1 A:ASN741 2.3 19.0 1.0
OD1 A:ASP739 2.3 16.7 1.0
OD1 A:ASP743 2.3 19.2 1.0
O A:LEU745 2.3 17.5 1.0
O A:HOH1427 2.4 22.7 1.0
CG A:ASP743 3.3 20.6 1.0
CG A:ASN741 3.4 22.5 1.0
CG A:ASP739 3.5 16.0 1.0
C A:LEU745 3.5 18.0 1.0
CG A:ASP747 3.5 18.9 1.0
OD2 A:ASP743 3.7 20.7 1.0
ND2 A:ASN741 3.8 27.8 1.0
N A:ASP747 3.9 17.2 1.0
CA A:ASP739 4.0 16.1 1.0
C A:ARG746 4.0 18.4 1.0
N A:LEU745 4.1 16.1 1.0
CA A:ASP747 4.1 16.9 1.0
CB A:ASP739 4.2 16.4 1.0
CA A:LEU745 4.2 17.1 1.0
O A:ARG746 4.3 18.0 1.0
N A:ASP743 4.3 18.3 1.0
OD2 A:ASP739 4.4 16.5 1.0
OD2 A:ASP747 4.4 19.6 1.0
CB A:ASP747 4.4 17.4 1.0
O A:PHE738 4.4 18.4 1.0
N A:ASN741 4.5 17.0 1.0
CB A:LEU745 4.5 17.1 1.0
C A:ASP739 4.5 16.6 1.0
N A:ARG746 4.5 17.7 1.0
O A:HOH1323 4.5 40.2 1.0
CB A:ASP743 4.5 19.3 1.0
OE2 A:GLU751 4.6 27.5 1.0
CB A:ASN741 4.6 19.0 1.0
CA A:ARG746 4.7 17.7 1.0
N A:TYR740 4.7 17.5 1.0
N A:TYR742 4.8 18.7 1.0
C A:ASN741 4.8 18.4 1.0
CA A:ASN741 4.8 17.8 1.0
CA A:ASP743 4.8 17.8 1.0
N A:GLY744 4.9 17.5 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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