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Calcium in PDB 7g52: Crystal Structure of Rat Autotaxin in Complex with 3-[(4-Chloro-5- Methyl-2-Propan-2-Ylphenoxy)Methyl]-1H-Pyridazin-6-One, I.E. Smiles O(CC1=Nnc(=O)C=C1)C1C(Cc(C(C1)C)Cl)C(C)C with IC50=0.043937 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-[(4-Chloro-5- Methyl-2-Propan-2-Ylphenoxy)Methyl]-1H-Pyridazin-6-One, I.E. Smiles O(CC1=Nnc(=O)C=C1)C1C(Cc(C(C1)C)Cl)C(C)C with IC50=0.043937 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-[(4-Chloro-5- Methyl-2-Propan-2-Ylphenoxy)Methyl]-1H-Pyridazin-6-One, I.E. Smiles O(CC1=Nnc(=O)C=C1)C1C(Cc(C(C1)C)Cl)C(C)C with IC50=0.043937 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-[(4-Chloro-5- Methyl-2-Propan-2-Ylphenoxy)Methyl]-1H-Pyridazin-6-One, I.E. Smiles O(CC1=Nnc(=O)C=C1)C1C(Cc(C(C1)C)Cl)C(C)C with IC50=0.043937 Microm, PDB code: 7g52 was solved by M.Stihle, J.Benz, D.Hunziker, W.Neidhart, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.94 / 1.71
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.982, 91.885, 119.819, 90, 90, 90
R / Rfree (%) 18.4 / 22.4

Other elements in 7g52:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-[(4-Chloro-5- Methyl-2-Propan-2-Ylphenoxy)Methyl]-1H-Pyridazin-6-One, I.E. Smiles O(CC1=Nnc(=O)C=C1)C1C(Cc(C(C1)C)Cl)C(C)C with IC50=0.043937 Microm also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 3-[(4-Chloro-5- Methyl-2-Propan-2-Ylphenoxy)Methyl]-1H-Pyridazin-6-One, I.E. Smiles O(CC1=Nnc(=O)C=C1)C1C(Cc(C(C1)C)Cl)C(C)C with IC50=0.043937 Microm (pdb code 7g52). 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 3-[(4-Chloro-5- Methyl-2-Propan-2-Ylphenoxy)Methyl]-1H-Pyridazin-6-One, I.E. Smiles O(CC1=Nnc(=O)C=C1)C1C(Cc(C(C1)C)Cl)C(C)C with IC50=0.043937 Microm, PDB code: 7g52:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g52

Go back to Calcium Binding Sites List in 7g52
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-[(4-Chloro-5- Methyl-2-Propan-2-Ylphenoxy)Methyl]-1H-Pyridazin-6-One, I.E. Smiles O(CC1=Nnc(=O)C=C1)C1C(Cc(C(C1)C)Cl)C(C)C with IC50=0.043937 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 3-[(4-Chloro-5- Methyl-2-Propan-2-Ylphenoxy)Methyl]-1H-Pyridazin-6-One, I.E. Smiles O(CC1=Nnc(=O)C=C1)C1C(Cc(C(C1)C)Cl)C(C)C with IC50=0.043937 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:28.8
occ:0.50
 OD1 A:ASP171 1.6 27.9 1.0
OG1 A:THR209 1.8 21.9 1.0
NE2 A:HIS359 2.0 15.9 1.0
OD2 A:ASP358 2.4 22.1 1.0
O A:HOH1009 2.7 40.0 1.0
CG A:ASP171 2.7 23.5 1.0
CB A:THR209 2.9 19.8 1.0
CE1 A:HIS359 2.9 14.9 1.0
CD2 A:HIS359 3.0 14.9 1.0
CG A:ASP358 3.1 19.0 1.0
CG2 A:THR209 3.2 23.2 1.0
OD2 A:ASP171 3.2 30.4 1.0
CA A:THR209 3.3 16.4 1.0
OD1 A:ASP358 3.4 19.2 1.0
N A:THR209 3.8 17.2 1.0
CB A:ASP171 3.9 19.2 1.0
ND1 A:HIS359 4.0 16.8 1.0
CG A:HIS359 4.1 15.8 1.0
OD1 A:ASP311 4.1 21.4 1.0
N A:GLY172 4.1 16.1 1.0
CA A:ASP171 4.2 18.2 1.0
CE1 A:HIS474 4.3 19.6 1.0
CB A:ASP358 4.4 18.2 1.0
CG A:ASP311 4.4 20.2 1.0
O A:HOH1003 4.5 23.7 1.0
C A:ASP171 4.5 17.3 1.0
ZN A:ZN904 4.5 21.8 1.0
NE2 A:HIS474 4.6 20.2 1.0
C A:THR209 4.7 17.1 1.0
C A:LYS208 4.7 16.9 1.0
CB A:ASP311 4.8 17.5 1.0
OH A:TYR306 4.9 21.6 1.0
OD2 A:ASP311 4.9 21.8 1.0
O A:HOH1480 4.9 33.3 1.0
CA A:GLY172 4.9 17.4 1.0

Calcium binding site 2 out of 2 in 7g52

Go back to Calcium Binding Sites List in 7g52
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-[(4-Chloro-5- Methyl-2-Propan-2-Ylphenoxy)Methyl]-1H-Pyridazin-6-One, I.E. Smiles O(CC1=Nnc(=O)C=C1)C1C(Cc(C(C1)C)Cl)C(C)C with IC50=0.043937 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 3-[(4-Chloro-5- Methyl-2-Propan-2-Ylphenoxy)Methyl]-1H-Pyridazin-6-One, I.E. Smiles O(CC1=Nnc(=O)C=C1)C1C(Cc(C(C1)C)Cl)C(C)C with IC50=0.043937 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:17.3
occ:1.00
 O A:HOH1417 2.3 22.8 1.0
OD1 A:ASP747 2.3 19.3 1.0
OD1 A:ASP739 2.3 17.2 1.0
O A:LEU745 2.3 16.7 1.0
OD1 A:ASN741 2.3 20.6 1.0
OD1 A:ASP743 2.4 18.6 1.0
CG A:ASP743 3.3 20.1 1.0
CG A:ASN741 3.4 19.9 1.0
C A:LEU745 3.5 16.2 1.0
CG A:ASP739 3.5 17.2 1.0
CG A:ASP747 3.5 18.9 1.0
OD2 A:ASP743 3.7 22.2 1.0
ND2 A:ASN741 3.8 22.6 1.0
N A:ASP747 4.0 16.7 1.0
CA A:ASP739 4.0 14.3 1.0
C A:ARG746 4.0 17.0 1.0
N A:LEU745 4.1 15.4 1.0
CA A:ASP747 4.1 18.0 1.0
O A:ARG746 4.2 17.0 1.0
CA A:LEU745 4.2 15.3 1.0
CB A:ASP739 4.2 16.3 1.0
N A:ASP743 4.2 16.9 1.0
OD2 A:ASP739 4.3 17.6 1.0
OD2 A:ASP747 4.4 20.1 1.0
CB A:LEU745 4.4 17.1 1.0
CB A:ASP747 4.4 18.8 1.0
N A:ARG746 4.4 16.3 1.0
N A:ASN741 4.5 16.3 1.0
O A:PHE738 4.5 15.3 1.0
C A:ASP739 4.5 16.9 1.0
CB A:ASP743 4.5 18.4 1.0
OE2 A:GLU751 4.5 27.9 1.0
O A:HOH1302 4.6 33.9 1.0
CA A:ARG746 4.7 16.1 1.0
CB A:ASN741 4.7 18.9 1.0
N A:TYR740 4.7 16.4 1.0
N A:TYR742 4.7 16.8 1.0
CA A:ASP743 4.8 16.8 1.0
N A:GLY744 4.9 15.9 1.0
C A:ASN741 4.9 18.3 1.0
CA A:ASN741 4.9 16.7 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 15:49:17 2025

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