Atomistry » Sodium » PDB 7g49-7g5t » 7g56
Atomistry »
  Sodium »
    PDB 7g49-7g5t »
      7g56 »

Sodium in PDB 7g56: Crystal Structure of Rat Autotaxin in Complex with A Dimer of [(2R,4S, 5S)-5-Ethynyl-1-Azabicyclo[2.2.2]Octan-2-Yl]Methyl N- Cyclohexylcarbamate, I.E. Smiles O=C(NC1CCCCC1) Oc[C@H]2C[C@@H]3CCN2C[C@@H]3C#Cc#C[C@H]4CN5CC[C@H]4C[C@@H]5COC(=O) NC6CCCCC6 with IC50=4.47875 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with A Dimer of [(2R,4S, 5S)-5-Ethynyl-1-Azabicyclo[2.2.2]Octan-2-Yl]Methyl N- Cyclohexylcarbamate, I.E. Smiles O=C(NC1CCCCC1) Oc[C@H]2C[C@@H]3CCN2C[C@@H]3C#Cc#C[C@H]4CN5CC[C@H]4C[C@@H]5COC(=O) NC6CCCCC6 with IC50=4.47875 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with A Dimer of [(2R,4S, 5S)-5-Ethynyl-1-Azabicyclo[2.2.2]Octan-2-Yl]Methyl N- Cyclohexylcarbamate, I.E. Smiles O=C(NC1CCCCC1) Oc[C@H]2C[C@@H]3CCN2C[C@@H]3C#Cc#C[C@H]4CN5CC[C@H]4C[C@@H]5COC(=O) NC6CCCCC6 with IC50=4.47875 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with A Dimer of [(2R,4S, 5S)-5-Ethynyl-1-Azabicyclo[2.2.2]Octan-2-Yl]Methyl N- Cyclohexylcarbamate, I.E. Smiles O=C(NC1CCCCC1) Oc[C@H]2C[C@@H]3CCN2C[C@@H]3C#Cc#C[C@H]4CN5CC[C@H]4C[C@@H]5COC(=O) NC6CCCCC6 with IC50=4.47875 Microm, PDB code: 7g56 was solved by M.Stihle, J.Benz, D.Hunziker, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.58 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.493, 92.418, 118.751, 90, 90, 90
R / Rfree (%) 19.2 / 23.3

Other elements in 7g56:

The structure of Crystal Structure of Rat Autotaxin in Complex with A Dimer of [(2R,4S, 5S)-5-Ethynyl-1-Azabicyclo[2.2.2]Octan-2-Yl]Methyl N- Cyclohexylcarbamate, I.E. Smiles O=C(NC1CCCCC1) Oc[C@H]2C[C@@H]3CCN2C[C@@H]3C#Cc#C[C@H]4CN5CC[C@H]4C[C@@H]5COC(=O) NC6CCCCC6 with IC50=4.47875 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with A Dimer of [(2R,4S, 5S)-5-Ethynyl-1-Azabicyclo[2.2.2]Octan-2-Yl]Methyl N- Cyclohexylcarbamate, I.E. Smiles O=C(NC1CCCCC1) Oc[C@H]2C[C@@H]3CCN2C[C@@H]3C#Cc#C[C@H]4CN5CC[C@H]4C[C@@H]5COC(=O) NC6CCCCC6 with IC50=4.47875 Microm (pdb code 7g56). 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 A Dimer of [(2R,4S, 5S)-5-Ethynyl-1-Azabicyclo[2.2.2]Octan-2-Yl]Methyl N- Cyclohexylcarbamate, I.E. Smiles O=C(NC1CCCCC1) Oc[C@H]2C[C@@H]3CCN2C[C@@H]3C#Cc#C[C@H]4CN5CC[C@H]4C[C@@H]5COC(=O) NC6CCCCC6 with IC50=4.47875 Microm, PDB code: 7g56:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g56

Go back to Sodium Binding Sites List in 7g56
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with A Dimer of [(2R,4S, 5S)-5-Ethynyl-1-Azabicyclo[2.2.2]Octan-2-Yl]Methyl N- Cyclohexylcarbamate, I.E. Smiles O=C(NC1CCCCC1) Oc[C@H]2C[C@@H]3CCN2C[C@@H]3C#Cc#C[C@H]4CN5CC[C@H]4C[C@@H]5COC(=O) NC6CCCCC6 with IC50=4.47875 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 A Dimer of [(2R,4S, 5S)-5-Ethynyl-1-Azabicyclo[2.2.2]Octan-2-Yl]Methyl N- Cyclohexylcarbamate, I.E. Smiles O=C(NC1CCCCC1) Oc[C@H]2C[C@@H]3CCN2C[C@@H]3C#Cc#C[C@H]4CN5CC[C@H]4C[C@@H]5COC(=O) NC6CCCCC6 with IC50=4.47875 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na904

b:46.5
occ:1.00
 O A:ASP672 2.3 38.7 1.0
O A:MET675 2.3 33.7 1.0
O A:HOH1377 2.4 45.1 1.0
O A:TYR669 2.5 38.9 1.0
O A:HOH1182 2.8 56.5 1.0
O A:HOH1394 2.8 51.5 1.0
C A:MET675 3.4 35.1 1.0
C A:ASP672 3.5 39.8 1.0
C A:TYR669 3.5 37.1 1.0
N A:MET675 4.1 37.1 1.0
N A:SER676 4.3 30.2 1.0
CA A:TYR669 4.3 33.8 1.0
CA A:MET675 4.3 34.5 1.0
C A:LYS673 4.3 41.4 1.0
CA A:LYS673 4.3 47.0 1.0
CA A:SER676 4.3 30.1 1.0
N A:LYS673 4.4 40.4 1.0
O A:LYS673 4.4 41.5 1.0
CA A:ASP672 4.5 38.0 1.0
N A:LYS670 4.5 38.7 1.0
O A:LYS670 4.6 40.1 1.0
N A:ASP672 4.6 41.6 1.0
CB A:TYR669 4.6 30.7 1.0
CB A:ASP672 4.7 36.3 1.0
CA A:LYS670 4.7 39.1 1.0
C A:LYS670 4.8 38.5 1.0
N A:GLN674 4.9 41.4 1.0
CB A:SER676 4.9 32.3 1.0
C A:GLN674 5.0 42.2 1.0

Sodium binding site 2 out of 2 in 7g56

Go back to Sodium Binding Sites List in 7g56
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with A Dimer of [(2R,4S, 5S)-5-Ethynyl-1-Azabicyclo[2.2.2]Octan-2-Yl]Methyl N- Cyclohexylcarbamate, I.E. Smiles O=C(NC1CCCCC1) Oc[C@H]2C[C@@H]3CCN2C[C@@H]3C#Cc#C[C@H]4CN5CC[C@H]4C[C@@H]5COC(=O) NC6CCCCC6 with IC50=4.47875 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 A Dimer of [(2R,4S, 5S)-5-Ethynyl-1-Azabicyclo[2.2.2]Octan-2-Yl]Methyl N- Cyclohexylcarbamate, I.E. Smiles O=C(NC1CCCCC1) Oc[C@H]2C[C@@H]3CCN2C[C@@H]3C#Cc#C[C@H]4CN5CC[C@H]4C[C@@H]5COC(=O) NC6CCCCC6 with IC50=4.47875 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:57.5
occ:1.00
 O A:HOH1397 2.3 54.4 1.0
O A:HOH1341 2.4 42.3 1.0
OG1 A:THR567 2.5 49.3 1.0
O A:THR567 2.5 42.0 1.0
O A:HOH1383 2.5 49.1 1.0
O A:ASN650 2.5 42.0 1.0
C A:THR567 3.3 47.9 1.0
C A:ASN650 3.4 39.7 1.0
CB A:THR567 3.6 53.2 1.0
N A:THR567 3.6 46.5 1.0
CA A:THR567 3.7 48.9 1.0
CB A:ASN650 3.8 48.6 1.0
O A:HOH1113 3.9 53.7 1.0
N A:CYS651 4.1 34.0 1.0
CA A:CYS651 4.1 39.3 1.0
CA A:ASN650 4.2 46.0 1.0
O A:HOH1176 4.3 50.7 1.0
N A:CYS568 4.4 40.5 1.0
N A:VAL652 4.5 34.5 1.0
C A:CYS651 4.7 36.5 1.0
CG2 A:THR567 4.8 54.3 1.0
CA A:CYS568 4.8 46.8 1.0
C A:CYS566 4.9 47.5 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 23:20:50 2025

Last articles

Zn in 9IRQ
Zn in 9IYX
Zn in 9J8P
Zn in 9IUU
Zn in 9GBF
Zn in 9G2V
Zn in 9G2L
Zn in 9G2X
Zn in 9G2Z
Zn in 9G2K
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy