Atomistry » Sodium » PDB 7f5i-7g32 » 7g2y
Atomistry »
  Sodium »
    PDB 7f5i-7g32 »
      7g2y »

Sodium in PDB 7g2y: Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm, PDB code: 7g2y 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) 48.68 / 1.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.882, 91.634, 119.543, 90, 90, 90
R / Rfree (%) 17.9 / 22

Other elements in 7g2y:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom
Potassium (K) 1 atom
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm (pdb code 7g2y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm, PDB code: 7g2y:

Sodium binding site 1 out of 1 in 7g2y

Go back to Sodium Binding Sites List in 7g2y
Sodium binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:30.4
occ:1.00
 OG A:SER807 2.2 24.0 1.0
O A:HOH1435 2.4 33.6 1.0
O A:SER804 2.4 22.9 1.0
O A:HOH1255 2.4 25.2 1.0
O A:ASN801 2.5 20.3 1.0
O A:HOH1151 2.6 26.7 1.0
C A:ASN801 3.3 20.9 1.0
CB A:SER807 3.3 24.3 1.0
C A:SER804 3.4 22.9 1.0
CA A:ASP802 3.8 24.7 1.0
N A:ASP802 3.9 21.8 1.0
N A:SER807 4.1 25.9 1.0
C A:ASP802 4.2 22.2 1.0
CA A:CYS805 4.2 25.5 1.0
CA A:SER807 4.2 27.5 1.0
O A:ASP802 4.2 20.6 1.0
N A:CYS805 4.2 24.4 1.0
CB A:ASN801 4.3 20.5 1.0
N A:SER804 4.3 20.2 1.0
CA A:ASN801 4.3 21.7 1.0
C A:CYS805 4.3 29.0 1.0
O A:HOH1188 4.3 37.3 1.0
CA A:SER804 4.4 21.6 1.0
O A:CYS805 4.5 27.5 1.0
CB A:SER804 4.7 25.7 1.0
O A:HOH1315 4.7 32.3 1.0
OD1 A:ASP802 4.7 32.8 1.0
O A:HOH1264 4.7 32.8 1.0
N A:ASN806 4.9 29.4 1.0
N A:GLU803 4.9 19.7 1.0
C A:SER807 5.0 29.0 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 23:09:26 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy