Atomistry » Calcium » PDB 7g78-7jlg » 7g7d
Atomistry »
  Calcium »
    PDB 7g78-7jlg »
      7g7d »

Calcium in PDB 7g7d: Crystal Structure of Rat Autotaxin in Complex with 5-[3-Oxo-3-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2-Yl]Propyl]-3H-1,3- Oxazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)CCC1=Cnc(=O)O1 with IC50=0.0580555 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-[3-Oxo-3-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2-Yl]Propyl]-3H-1,3- Oxazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)CCC1=Cnc(=O)O1 with IC50=0.0580555 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-[3-Oxo-3-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2-Yl]Propyl]-3H-1,3- Oxazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)CCC1=Cnc(=O)O1 with IC50=0.0580555 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-[3-Oxo-3-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2-Yl]Propyl]-3H-1,3- Oxazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)CCC1=Cnc(=O)O1 with IC50=0.0580555 Microm, PDB code: 7g7d 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) 45.71 / 2.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.702, 91.424, 118.999, 90, 90, 90
R / Rfree (%) 18.9 / 23.7

Other elements in 7g7d:

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-[3-Oxo-3-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2-Yl]Propyl]-3H-1,3- Oxazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)CCC1=Cnc(=O)O1 with IC50=0.0580555 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom
Potassium (K) 1 atom
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 5-[3-Oxo-3-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2-Yl]Propyl]-3H-1,3- Oxazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)CCC1=Cnc(=O)O1 with IC50=0.0580555 Microm (pdb code 7g7d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Rat Autotaxin in Complex with 5-[3-Oxo-3-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2-Yl]Propyl]-3H-1,3- Oxazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)CCC1=Cnc(=O)O1 with IC50=0.0580555 Microm, PDB code: 7g7d:

Calcium binding site 1 out of 1 in 7g7d

Go back to Calcium Binding Sites List in 7g7d
Calcium binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with 5-[3-Oxo-3-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2-Yl]Propyl]-3H-1,3- Oxazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)CCC1=Cnc(=O)O1 with IC50=0.0580555 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 5-[3-Oxo-3-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2-Yl]Propyl]-3H-1,3- Oxazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)CCC1=Cnc(=O)O1 with IC50=0.0580555 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:31.3
occ:1.00
 OD1 A:ASP747 2.2 33.5 1.0
OD1 A:ASP743 2.3 31.8 1.0
O A:HOH1146 2.3 31.4 1.0
O A:LEU745 2.3 29.7 1.0
OD1 A:ASN741 2.4 32.9 1.0
OD1 A:ASP739 2.4 25.3 1.0
CG A:ASP743 3.3 30.6 1.0
C A:LEU745 3.4 27.4 1.0
CG A:ASN741 3.5 33.9 1.0
CG A:ASP747 3.5 37.9 1.0
CG A:ASP739 3.6 27.7 1.0
OD2 A:ASP743 3.7 35.4 1.0
N A:ASP747 3.8 28.6 1.0
ND2 A:ASN741 3.9 35.3 1.0
CA A:ASP739 4.0 29.8 1.0
C A:ARG746 4.0 32.1 1.0
N A:LEU745 4.1 26.9 1.0
CA A:ASP747 4.1 32.8 1.0
CA A:LEU745 4.2 28.1 1.0
CB A:ASP739 4.3 27.2 1.0
O A:ARG746 4.3 31.0 1.0
N A:ASP743 4.3 30.1 1.0
OD2 A:ASP747 4.3 36.8 1.0
CB A:ASP747 4.4 33.9 1.0
N A:ARG746 4.4 28.4 1.0
CB A:LEU745 4.5 28.0 1.0
O A:PHE738 4.5 27.1 1.0
N A:ASN741 4.5 28.8 1.0
C A:ASP739 4.5 30.9 1.0
OD2 A:ASP739 4.5 27.6 1.0
CB A:ASP743 4.6 30.1 1.0
CA A:ARG746 4.7 29.8 1.0
N A:TYR742 4.7 31.1 1.0
CB A:ASN741 4.7 29.8 1.0
N A:TYR740 4.8 28.4 1.0
OE2 A:GLU751 4.8 57.0 1.0
CA A:ASP743 4.8 30.4 1.0
C A:ASN741 4.8 32.1 1.0
N A:GLY744 4.9 30.2 1.0
CA A:ASN741 4.9 30.7 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 22:37:40 2025

Last articles

Mg in 4J5I
Mg in 4J4B
Mg in 4J3N
Mg in 4J49
Mg in 4J43
Mg in 4J1O
Mg in 4J3B
Mg in 4J0Q
Mg in 4J0B
Mg in 4J03
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy