Atomistry » Sodium » PDB 7g5u-7g6x » 7g6c
Atomistry »
  Sodium »
    PDB 7g5u-7g6x »
      7g6c »

Sodium in PDB 7g6c: Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Cyano-5-Methylphenoxy)Methyl]-5-Pyrrolidin-1-Yl-1,3-Oxazole-4- Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc(=C(O1)N1CCCC1) C#N)C)C#N with IC50=0.0607829 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Cyano-5-Methylphenoxy)Methyl]-5-Pyrrolidin-1-Yl-1,3-Oxazole-4- Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc(=C(O1)N1CCCC1) C#N)C)C#N with IC50=0.0607829 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Cyano-5-Methylphenoxy)Methyl]-5-Pyrrolidin-1-Yl-1,3-Oxazole-4- Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc(=C(O1)N1CCCC1) C#N)C)C#N with IC50=0.0607829 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Cyano-5-Methylphenoxy)Methyl]-5-Pyrrolidin-1-Yl-1,3-Oxazole-4- Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc(=C(O1)N1CCCC1) C#N)C)C#N with IC50=0.0607829 Microm, PDB code: 7g6c was solved by M.Stihle, J.Benz, D.Hunziker, T.Lubbers, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.68 / 2.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.73, 91.354, 119.293, 90, 90, 90
R / Rfree (%) 19.3 / 25.1

Other elements in 7g6c:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Cyano-5-Methylphenoxy)Methyl]-5-Pyrrolidin-1-Yl-1,3-Oxazole-4- Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc(=C(O1)N1CCCC1) C#N)C)C#N with IC50=0.0607829 Microm also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Cyano-5-Methylphenoxy)Methyl]-5-Pyrrolidin-1-Yl-1,3-Oxazole-4- Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc(=C(O1)N1CCCC1) C#N)C)C#N with IC50=0.0607829 Microm (pdb code 7g6c). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Cyano-5-Methylphenoxy)Methyl]-5-Pyrrolidin-1-Yl-1,3-Oxazole-4- Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc(=C(O1)N1CCCC1) C#N)C)C#N with IC50=0.0607829 Microm, PDB code: 7g6c:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g6c

Go back to Sodium Binding Sites List in 7g6c
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Cyano-5-Methylphenoxy)Methyl]-5-Pyrrolidin-1-Yl-1,3-Oxazole-4- Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc(=C(O1)N1CCCC1) C#N)C)C#N with IC50=0.0607829 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-[(2-Tert-Butyl-4- Cyano-5-Methylphenoxy)Methyl]-5-Pyrrolidin-1-Yl-1,3-Oxazole-4- Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc(=C(O1)N1CCCC1) C#N)C)C#N with IC50=0.0607829 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na904

b:39.2
occ:1.00
 OG A:SER807 2.2 38.5 1.0
O A:SER804 2.3 35.7 1.0
O A:HOH1266 2.5 31.8 1.0
O A:ASN801 2.6 30.9 1.0
O A:HOH1158 2.8 37.1 1.0
C A:SER804 3.4 39.7 1.0
CB A:SER807 3.5 39.1 1.0
C A:ASN801 3.5 32.5 1.0
CA A:ASP802 3.8 36.2 1.0
N A:SER807 4.0 40.5 1.0
O A:ASP802 4.0 38.2 1.0
N A:ASP802 4.0 34.1 1.0
C A:ASP802 4.1 37.2 1.0
CA A:CYS805 4.1 40.1 1.0
N A:CYS805 4.2 41.3 1.0
C A:CYS805 4.2 41.1 1.0
CA A:SER807 4.3 40.2 1.0
O A:CYS805 4.3 41.1 1.0
N A:SER804 4.4 37.2 1.0
CB A:ASN801 4.4 32.5 1.0
CA A:SER804 4.5 37.9 1.0
CA A:ASN801 4.6 32.6 1.0
N A:ASN806 4.7 43.5 1.0
O A:HOH1111 4.7 31.9 1.0
OD1 A:ASP802 4.9 40.7 1.0
N A:GLU803 4.9 36.6 1.0
CB A:SER804 5.0 40.0 1.0

Sodium binding site 2 out of 2 in 7g6c

Go back to Sodium Binding Sites List in 7g6c
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Cyano-5-Methylphenoxy)Methyl]-5-Pyrrolidin-1-Yl-1,3-Oxazole-4- Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc(=C(O1)N1CCCC1) C#N)C)C#N with IC50=0.0607829 Microm


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-4- Cyano-5-Methylphenoxy)Methyl]-5-Pyrrolidin-1-Yl-1,3-Oxazole-4- Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc(=C(O1)N1CCCC1) C#N)C)C#N with IC50=0.0607829 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:20.1
occ:1.00
 O A:MET675 2.2 43.7 1.0
O A:HOH1197 2.2 39.8 1.0
O A:ASP672 2.3 38.0 1.0
O A:TYR669 2.4 41.1 1.0
O A:HOH1260 2.6 37.0 1.0
C A:MET675 3.3 40.3 1.0
C A:ASP672 3.5 40.3 1.0
C A:TYR669 3.6 42.4 1.0
N A:SER676 4.1 37.3 1.0
CA A:SER676 4.2 34.3 1.0
N A:MET675 4.2 45.3 1.0
CA A:LYS673 4.2 47.2 1.0
C A:LYS673 4.2 46.9 1.0
N A:LYS673 4.3 42.6 1.0
CA A:MET675 4.3 41.2 1.0
O A:LYS673 4.3 46.5 1.0
O A:LYS670 4.4 44.9 1.0
CA A:TYR669 4.4 39.5 1.0
CA A:ASP672 4.5 39.6 1.0
N A:LYS670 4.6 43.8 1.0
C A:LYS670 4.7 43.8 1.0
CA A:LYS670 4.7 44.6 1.0
CB A:SER676 4.7 31.8 1.0
CB A:ASP672 4.7 38.1 1.0
N A:ASP672 4.7 43.9 1.0
N A:GLN674 4.8 49.4 1.0
C A:GLN674 4.8 49.6 1.0
CB A:TYR669 4.8 37.7 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: Sat Feb 8 23:25:46 2025

Last articles

Mg in 4L9Z
Mg in 4L9Y
Mg in 4LA6
Mg in 4L9W
Mg in 4L81
Mg in 4L9S
Mg in 4L8N
Mg in 4L87
Mg in 4L8G
Mg in 4L80
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy