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Calcium in PDB 7g5q: Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm, PDB code: 7g5q was solved by M.Stihle, J.Benz, D.Hunziker, H.Kuhne, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.69 / 1.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.045, 92.177, 119.482, 90, 90, 90
R / Rfree (%) 19 / 22.4

Other elements in 7g5q:

The structure of Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Zinc (Zn) 1 atom
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm (pdb code 7g5q). 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 (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm, PDB code: 7g5q:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g5q

Go back to Calcium Binding Sites List in 7g5q
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 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 (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:25.8
occ:1.00
 OD1 A:ASP171 1.7 16.6 1.0
NE2 A:HIS359 2.0 10.6 1.0
OG1 A:THR209 2.1 17.5 1.0
OD2 A:ASP358 2.2 13.8 1.0
CG A:ASP171 2.8 18.4 1.0
CE1 A:HIS359 2.8 11.2 1.0
CG A:ASP358 3.0 12.1 1.0
CB A:THR209 3.0 14.0 1.0
CD2 A:HIS359 3.0 10.9 1.0
CG2 A:THR209 3.0 14.6 1.0
OD1 A:ASP358 3.3 11.3 1.0
OD2 A:ASP171 3.3 26.5 1.0
CA A:THR209 3.4 11.5 1.0
ND1 A:HIS359 3.9 11.9 1.0
CB A:ASP171 3.9 14.2 1.0
OD1 A:ASP311 4.0 15.2 1.0
N A:GLY172 4.0 12.0 1.0
CG A:HIS359 4.0 10.6 1.0
N A:THR209 4.0 12.2 1.0
CA A:ASP171 4.1 12.6 1.0
O A:HOH1032 4.2 26.8 1.0
CB A:ASP358 4.3 11.1 1.0
CE1 A:HIS474 4.3 16.4 1.0
O A:HOH1497 4.4 27.2 1.0
CG A:ASP311 4.4 12.6 1.0
C A:ASP171 4.4 12.4 1.0
ZN A:ZN906 4.5 14.2 1.0
NE2 A:HIS474 4.6 12.9 1.0
C A:THR209 4.6 12.1 1.0
CB A:ASP311 4.8 10.9 1.0
C A:LYS208 4.8 10.8 1.0
CA A:GLY172 4.8 11.9 1.0
OD2 A:ASP311 4.9 14.5 1.0

Calcium binding site 2 out of 2 in 7g5q

Go back to Calcium Binding Sites List in 7g5q
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 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 (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:12.2
occ:1.00
 OD1 A:ASP747 2.3 12.1 1.0
O A:LEU745 2.3 12.6 1.0
OD1 A:ASN741 2.3 14.2 1.0
OD1 A:ASP739 2.3 11.9 1.0
OD1 A:ASP743 2.4 12.2 1.0
O A:HOH1474 2.4 16.0 1.0
CG A:ASP743 3.4 13.1 1.0
CG A:ASN741 3.4 15.2 1.0
C A:LEU745 3.5 11.0 1.0
CG A:ASP739 3.5 10.9 1.0
CG A:ASP747 3.5 11.4 1.0
OD2 A:ASP743 3.8 13.8 1.0
ND2 A:ASN741 3.9 17.0 1.0
N A:ASP747 3.9 11.7 1.0
CA A:ASP739 3.9 9.7 1.0
C A:ARG746 4.0 12.8 1.0
CA A:ASP747 4.1 11.6 1.0
N A:LEU745 4.1 10.1 1.0
O A:ARG746 4.2 13.3 1.0
CB A:ASP739 4.2 10.8 1.0
CA A:LEU745 4.2 10.9 1.0
N A:ASP743 4.3 11.6 1.0
O A:PHE738 4.4 10.7 1.0
CB A:ASP747 4.4 12.9 1.0
C A:ASP739 4.4 10.6 1.0
OD2 A:ASP747 4.4 14.6 1.0
OD2 A:ASP739 4.4 11.3 1.0
N A:ASN741 4.5 12.6 1.0
CB A:LEU745 4.5 11.7 1.0
N A:ARG746 4.5 11.3 1.0
CB A:ASP743 4.6 12.0 1.0
OE2 A:GLU751 4.6 17.6 1.0
O A:HOH1294 4.6 25.1 1.0
N A:TYR740 4.7 11.1 1.0
CA A:ARG746 4.7 11.6 1.0
CB A:ASN741 4.7 12.9 1.0
N A:TYR742 4.8 12.0 1.0
CA A:ASP743 4.8 11.7 1.0
N A:GLY744 4.9 11.6 1.0
CA A:ASN741 4.9 13.1 1.0
C A:ASN741 4.9 12.0 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 22:30:02 2025

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