Atomistry » Calcium » PDB 7f9g-7g2q » 7g2q
Atomistry »
  Calcium »
    PDB 7f9g-7g2q »
      7g2q »

Calcium in PDB 7g2q: Crystal Structure of Rat Autotaxin in Complex with 1-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]Piperidine-4-Sulfonamide, I.E. Smiles N1(C(=O)N2CC3=C(Cn(C3)C(=O)C3CC(Nc(C3)C3CC3)OCC3CCOCC3) C2)Cc[C@@H](CC1)S(=O)(=O)N with IC50=0.00248328 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]Piperidine-4-Sulfonamide, I.E. Smiles N1(C(=O)N2CC3=C(Cn(C3)C(=O)C3CC(Nc(C3)C3CC3)OCC3CCOCC3) C2)Cc[C@@H](CC1)S(=O)(=O)N with IC50=0.00248328 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]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]Piperidine-4-Sulfonamide, I.E. Smiles N1(C(=O)N2CC3=C(Cn(C3)C(=O)C3CC(Nc(C3)C3CC3)OCC3CCOCC3) C2)Cc[C@@H](CC1)S(=O)(=O)N with IC50=0.00248328 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]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]Piperidine-4-Sulfonamide, I.E. Smiles N1(C(=O)N2CC3=C(Cn(C3)C(=O)C3CC(Nc(C3)C3CC3)OCC3CCOCC3) C2)Cc[C@@H](CC1)S(=O)(=O)N with IC50=0.00248328 Microm, PDB code: 7g2q 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) 43.20 / 1.83
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.089, 91.991, 120.355, 90, 90, 90
R / Rfree (%) 19.7 / 24.1

Other elements in 7g2q:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1-[2-[2- Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]Piperidine-4-Sulfonamide, I.E. Smiles N1(C(=O)N2CC3=C(Cn(C3)C(=O)C3CC(Nc(C3)C3CC3)OCC3CCOCC3) C2)Cc[C@@H](CC1)S(=O)(=O)N with IC50=0.00248328 Microm also contains other interesting chemical elements:

Sodium (Na) 1 atom
Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom
Potassium (K) 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]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]Piperidine-4-Sulfonamide, I.E. Smiles N1(C(=O)N2CC3=C(Cn(C3)C(=O)C3CC(Nc(C3)C3CC3)OCC3CCOCC3) C2)Cc[C@@H](CC1)S(=O)(=O)N with IC50=0.00248328 Microm (pdb code 7g2q). 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]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]Piperidine-4-Sulfonamide, I.E. Smiles N1(C(=O)N2CC3=C(Cn(C3)C(=O)C3CC(Nc(C3)C3CC3)OCC3CCOCC3) C2)Cc[C@@H](CC1)S(=O)(=O)N with IC50=0.00248328 Microm, PDB code: 7g2q:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g2q

Go back to Calcium Binding Sites List in 7g2q
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]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]Piperidine-4-Sulfonamide, I.E. Smiles N1(C(=O)N2CC3=C(Cn(C3)C(=O)C3CC(Nc(C3)C3CC3)OCC3CCOCC3) C2)Cc[C@@H](CC1)S(=O)(=O)N with IC50=0.00248328 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]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]Piperidine-4-Sulfonamide, I.E. Smiles N1(C(=O)N2CC3=C(Cn(C3)C(=O)C3CC(Nc(C3)C3CC3)OCC3CCOCC3) C2)Cc[C@@H](CC1)S(=O)(=O)N with IC50=0.00248328 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:29.5
occ:1.00
 OD1 A:ASP171 1.8 29.0 1.0
OG1 A:THR209 1.9 23.1 1.0
NE2 A:HIS359 2.1 22.5 1.0
OD2 A:ASP358 2.3 22.1 1.0
CG A:ASP171 2.6 25.9 1.0
CB A:THR209 2.9 21.4 1.0
OD2 A:ASP171 2.9 36.2 1.0
CE1 A:HIS359 3.0 21.2 1.0
CG A:ASP358 3.0 20.4 1.0
CD2 A:HIS359 3.1 20.4 1.0
OD1 A:ASP358 3.2 20.0 1.0
CG2 A:THR209 3.2 22.8 1.0
CA A:THR209 3.3 23.2 1.0
O38 A:XF3902 3.9 37.2 1.0
N A:THR209 3.9 21.6 1.0
CB A:ASP171 4.0 23.8 1.0
ND1 A:HIS359 4.0 21.9 1.0
CG A:HIS359 4.1 19.8 1.0
OD1 A:ASP311 4.2 23.2 1.0
N A:GLY172 4.3 20.4 1.0
CA A:ASP171 4.3 21.8 1.0
CB A:ASP358 4.3 19.7 1.0
CE1 A:HIS474 4.3 24.9 1.0
C34 A:XF3902 4.4 38.6 1.0
ZN A:ZN906 4.5 23.6 1.0
CG A:ASP311 4.5 20.6 1.0
NE2 A:HIS474 4.5 24.3 1.0
C A:THR209 4.6 21.6 1.0
C A:ASP171 4.7 22.2 1.0
C A:LYS208 4.8 22.4 1.0
O A:HOH1003 4.8 32.7 1.0
O A:THR209 4.9 21.2 1.0
CB A:ASP311 4.9 20.4 1.0
OD2 A:ASP311 4.9 22.7 1.0

Calcium binding site 2 out of 2 in 7g2q

Go back to Calcium Binding Sites List in 7g2q
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]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]Piperidine-4-Sulfonamide, I.E. Smiles N1(C(=O)N2CC3=C(Cn(C3)C(=O)C3CC(Nc(C3)C3CC3)OCC3CCOCC3) C2)Cc[C@@H](CC1)S(=O)(=O)N with IC50=0.00248328 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]-1,3,4,6- Tetrahydropyrrolo[3,4-C]Pyrrole-5-Carbonyl]Piperidine-4-Sulfonamide, I.E. Smiles N1(C(=O)N2CC3=C(Cn(C3)C(=O)C3CC(Nc(C3)C3CC3)OCC3CCOCC3) C2)Cc[C@@H](CC1)S(=O)(=O)N with IC50=0.00248328 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:20.4
occ:1.00
 O A:HOH1366 2.2 25.9 1.0
OD1 A:ASP739 2.3 21.2 1.0
O A:LEU745 2.3 20.0 1.0
OD1 A:ASP747 2.3 21.4 1.0
OD1 A:ASN741 2.3 23.7 1.0
OD1 A:ASP743 2.4 23.8 1.0
CG A:ASP743 3.3 22.7 1.0
CG A:ASN741 3.4 24.0 1.0
CG A:ASP739 3.4 20.7 1.0
C A:LEU745 3.4 21.5 1.0
CG A:ASP747 3.5 22.2 1.0
OD2 A:ASP743 3.7 24.1 1.0
ND2 A:ASN741 3.8 22.8 1.0
N A:ASP747 3.9 19.8 1.0
CA A:ASP739 3.9 19.5 1.0
C A:ARG746 4.0 20.6 1.0
N A:LEU745 4.1 20.1 1.0
CA A:ASP747 4.1 20.9 1.0
CB A:ASP739 4.2 19.9 1.0
O A:ARG746 4.2 19.9 1.0
CA A:LEU745 4.2 21.1 1.0
N A:ASP743 4.3 20.3 1.0
OD2 A:ASP739 4.4 21.5 1.0
OD2 A:ASP747 4.4 22.8 1.0
O A:PHE738 4.4 17.8 1.0
CB A:ASP747 4.4 21.4 1.0
C A:ASP739 4.5 19.9 1.0
N A:ARG746 4.5 20.8 1.0
N A:ASN741 4.5 23.4 1.0
CB A:LEU745 4.5 23.8 1.0
CB A:ASP743 4.5 21.5 1.0
OE2 A:GLU751 4.6 32.7 1.0
CB A:ASN741 4.7 22.7 1.0
N A:TYR742 4.7 23.7 1.0
CA A:ARG746 4.7 21.0 1.0
O A:HOH1335 4.7 34.1 1.0
N A:TYR740 4.7 22.1 1.0
CA A:ASP743 4.8 20.2 1.0
C A:ASN741 4.9 24.9 1.0
N A:GLY744 4.9 19.0 1.0
CA A:ASN741 4.9 22.6 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 15:33:32 2025

Last articles

Na in 7G3M
Na in 7G37
Na in 7G3E
Na in 7G3H
Na in 7G3L
Na in 7G34
Na in 7G3J
Na in 7G3K
Na in 7G39
Na in 7G3I
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy