Atomistry » Calcium » PDB 7g64-7g77 » 7g6a
Atomistry »
  Calcium »
    PDB 7g64-7g77 »
      7g6a »

Calcium in PDB 7g6a: Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm, PDB code: 7g6a 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) 45.67 / 1.63
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.657, 91.334, 118.662, 90, 90, 90
R / Rfree (%) 19.2 / 22

Other elements in 7g6a:

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Sodium (Na) 2 atoms
Fluorine (F) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm (pdb code 7g6a). 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 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm, PDB code: 7g6a:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g6a

Go back to Calcium Binding Sites List in 7g6a
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 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 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:27.4
occ:1.00
 OD1 A:ASP171 1.7 20.5 1.0
OG1 A:THR209 1.9 18.1 1.0
NE2 A:HIS359 2.1 12.0 1.0
OD2 A:ASP358 2.2 17.7 1.0
CG A:ASP171 2.7 20.3 1.0
CB A:THR209 2.9 16.3 1.0
CE1 A:HIS359 2.9 13.5 1.0
CD2 A:HIS359 3.0 12.9 1.0
CG A:ASP358 3.1 16.1 1.0
CG2 A:THR209 3.1 18.7 1.0
OD2 A:ASP171 3.2 28.8 1.0
OD1 A:ASP358 3.3 13.6 1.0
CA A:THR209 3.4 14.2 1.0
O A:HOH1018 3.7 34.7 1.0
CB A:ASP171 4.0 15.5 1.0
ND1 A:HIS359 4.0 13.3 1.0
N A:THR209 4.0 12.9 1.0
OD2 A:ASP311 4.0 15.8 1.0
N A:GLY172 4.1 12.3 1.0
CG A:HIS359 4.1 12.7 1.0
CA A:ASP171 4.2 13.9 1.0
O A:HOH1004 4.3 30.3 1.0
CE1 A:HIS474 4.4 13.0 1.0
CG A:ASP311 4.4 15.3 1.0
CB A:ASP358 4.4 14.5 1.0
ZN A:ZN906 4.5 15.8 1.0
C A:ASP171 4.5 13.7 1.0
O A:HOH1419 4.5 27.3 1.0
NE2 A:HIS474 4.5 13.2 1.0
C A:THR209 4.7 14.1 1.0
CB A:ASP311 4.8 14.0 1.0
C A:LYS208 4.8 13.0 1.0
OH A:TYR306 4.9 25.9 1.0
OD1 A:ASP311 4.9 17.6 1.0
CA A:GLY172 4.9 12.1 1.0

Calcium binding site 2 out of 2 in 7g6a

Go back to Calcium Binding Sites List in 7g6a
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 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 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:13.8
occ:1.00
 OD1 A:ASP739 2.3 12.9 1.0
O A:LEU745 2.3 13.6 1.0
OD1 A:ASP747 2.3 14.5 1.0
OD1 A:ASN741 2.3 14.9 1.0
O A:HOH1398 2.3 16.8 1.0
OD1 A:ASP743 2.4 14.2 1.0
CG A:ASP743 3.3 16.1 1.0
CG A:ASN741 3.4 17.5 1.0
CG A:ASP739 3.4 13.6 1.0
C A:LEU745 3.4 12.5 1.0
CG A:ASP747 3.5 14.0 1.0
OD2 A:ASP743 3.7 17.7 1.0
ND2 A:ASN741 3.9 20.5 1.0
N A:ASP747 3.9 12.8 1.0
CA A:ASP739 4.0 11.4 1.0
C A:ARG746 4.0 13.8 1.0
N A:LEU745 4.1 12.3 1.0
CA A:ASP747 4.1 13.1 1.0
O A:ARG746 4.2 13.4 1.0
CA A:LEU745 4.2 13.3 1.0
CB A:ASP739 4.2 12.5 1.0
N A:ASP743 4.3 13.4 1.0
OD2 A:ASP739 4.4 12.8 1.0
OD2 A:ASP747 4.4 15.7 1.0
O A:PHE738 4.4 12.0 1.0
CB A:ASP747 4.4 13.5 1.0
CB A:LEU745 4.5 13.4 1.0
C A:ASP739 4.5 11.7 1.0
N A:ASN741 4.5 14.3 1.0
N A:ARG746 4.5 13.2 1.0
CB A:ASP743 4.6 14.9 1.0
OE2 A:GLU751 4.6 27.0 1.0
O A:HOH1397 4.7 29.1 1.0
CB A:ASN741 4.7 15.7 1.0
N A:TYR740 4.7 11.9 1.0
CA A:ARG746 4.7 13.8 1.0
N A:TYR742 4.8 13.4 1.0
CA A:ASP743 4.8 14.6 1.0
C A:ASN741 4.9 15.0 1.0
CA A:ASN741 4.9 14.4 1.0
N A:GLY744 4.9 14.2 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: Wed Jul 9 22:32:49 2025

Last articles

Mg in 5E50
Mg in 5E4R
Mg in 5E4F
Mg in 5E4X
Mg in 5E41
Mg in 5E3I
Mg in 5E3H
Mg in 5E3C
Mg in 5E3A
Mg in 5E36
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy