Atomistry » Sodium » PDB 7g33-7g48 » 7g3t
Atomistry »
  Sodium »
    PDB 7g33-7g48 »
      7g3t »

Sodium in PDB 7g3t: Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm, PDB code: 7g3t was solved by M.Stihle, J.Benz, D.Hunziker, E.Pinard, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.92 / 1.33
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.77, 91.69, 120.29, 90, 90, 90
R / Rfree (%) 13.5 / 17.2

Other elements in 7g3t:

The structure of Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 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 (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm (pdb code 7g3t). 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 (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm, PDB code: 7g3t:

Sodium binding site 1 out of 1 in 7g3t

Go back to Sodium Binding Sites List in 7g3t
Sodium binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 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 (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na903

b:24.9
occ:1.00
 OG A:SER807 2.3 20.8 1.0
O A:SER804 2.4 16.4 1.0
O A:HOH1673 2.4 32.4 1.0
O A:ASN801 2.4 16.0 1.0
O A:HOH1487 2.5 28.1 1.0
O A:HOH1325 2.5 26.2 1.0
C A:ASN801 3.3 14.3 1.0
CB A:SER807 3.4 18.0 1.0
C A:SER804 3.5 17.1 1.0
CA A:ASP802 3.8 17.2 1.0
N A:ASP802 3.9 15.2 1.0
O A:HOH1768 4.0 36.5 1.0
N A:SER807 4.0 17.4 1.0
C A:ASP802 4.2 15.1 1.0
CA A:CYS805 4.2 17.5 1.0
O A:ASP802 4.2 15.0 1.0
CA A:SER807 4.2 18.1 1.0
CB A:ASN801 4.3 16.5 1.0
O A:HOH1155 4.3 32.6 1.0
N A:CYS805 4.3 16.0 1.0
N A:SER804 4.3 13.8 1.0
CA A:ASN801 4.3 15.5 1.0
C A:CYS805 4.4 18.2 1.0
CA A:SER804 4.4 15.2 1.0
O A:CYS805 4.5 21.0 1.0
OD1 A:ASP802 4.6 24.8 1.0
CB A:SER804 4.7 15.3 1.0
O A:HOH1294 4.7 27.4 1.0
O A:HOH1404 4.8 27.6 1.0
N A:ASN806 4.9 17.9 1.0
C A:SER807 4.9 20.3 1.0
N A:GLU803 5.0 13.7 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 23:15:13 2025

Last articles

Na in 7G58
Na in 7G53
Na in 7G51
Na in 7G5C
Na in 7G4Q
Na in 7G4Z
Na in 7G55
Na in 7G4S
Na in 7G4X
Na in 7G52
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy