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Calcium in PDB 7g2n: Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 Microm, PDB code: 7g2n was solved by M.Stihle, J.Benz, D.Hunziker, P.Mattei, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.61 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.952, 91.409, 119.249, 90, 90, 90
R / Rfree (%) 19.9 / 25.9

Other elements in 7g2n:

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 Microm also contains other interesting chemical elements:

Fluorine (F) 4 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 5-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 Microm (pdb code 7g2n). 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-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 Microm, PDB code: 7g2n:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g2n

Go back to Calcium Binding Sites List in 7g2n
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 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-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:71.6
occ:1.00
 OD1 A:ASP171 1.9 47.6 1.0
OG1 A:THR209 2.1 45.6 1.0
NE2 A:HIS359 2.3 38.0 1.0
OD2 A:ASP358 2.4 49.4 1.0
CG A:ASP171 2.9 45.6 1.0
CB A:THR209 2.9 42.9 1.0
CE1 A:HIS359 3.1 36.4 1.0
CG2 A:THR209 3.1 41.2 1.0
CG A:ASP358 3.2 42.7 1.0
CD2 A:HIS359 3.3 38.9 1.0
OD2 A:ASP171 3.3 50.9 1.0
CA A:THR209 3.4 44.0 1.0
OD1 A:ASP358 3.5 43.2 1.0
N A:THR209 3.9 44.0 1.0
CB A:ASP171 4.1 46.6 1.0
OD1 A:ASP311 4.1 41.9 1.0
ND1 A:HIS359 4.2 38.3 1.0
N A:GLY172 4.2 39.7 1.0
CG A:HIS359 4.3 36.9 1.0
CA A:ASP171 4.3 44.2 1.0
CG A:ASP311 4.4 44.2 1.0
O A:HOH1002 4.4 47.7 1.0
CE1 A:HIS474 4.5 41.8 1.0
CB A:ASP358 4.5 40.6 1.0
ZN A:ZN903 4.6 45.1 1.0
NE2 A:HIS474 4.6 42.0 1.0
OH A:TYR306 4.7 54.8 1.0
C A:THR209 4.7 41.7 1.0
CB A:ASP311 4.7 44.1 1.0
C A:ASP171 4.7 42.7 1.0
C A:LYS208 4.7 44.5 1.0
O A:HOH1176 4.8 40.8 1.0
OD2 A:ASP311 4.9 47.9 1.0

Calcium binding site 2 out of 2 in 7g2n

Go back to Calcium Binding Sites List in 7g2n
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 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-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:42.1
occ:1.00
 OD1 A:ASP747 2.2 42.2 1.0
O A:HOH1091 2.2 41.4 1.0
OD1 A:ASN741 2.3 47.5 1.0
O A:LEU745 2.3 38.8 1.0
OD1 A:ASP739 2.3 42.1 1.0
OD1 A:ASP743 2.4 45.2 1.0
CG A:ASP743 3.3 41.0 1.0
CG A:ASN741 3.4 41.8 1.0
CG A:ASP747 3.4 43.5 1.0
CG A:ASP739 3.4 40.9 1.0
C A:LEU745 3.5 40.5 1.0
OD2 A:ASP743 3.7 39.9 1.0
ND2 A:ASN741 3.8 44.6 1.0
N A:ASP747 3.9 38.0 1.0
CA A:ASP739 3.9 41.6 1.0
N A:LEU745 4.0 40.2 1.0
CA A:ASP747 4.1 41.5 1.0
C A:ARG746 4.1 41.1 1.0
CB A:ASP739 4.1 40.9 1.0
CA A:LEU745 4.2 41.5 1.0
OD2 A:ASP747 4.2 39.8 1.0
N A:ASP743 4.3 38.9 1.0
O A:PHE738 4.3 37.2 1.0
OD2 A:ASP739 4.3 42.6 1.0
CB A:ASP747 4.3 42.4 1.0
O A:ARG746 4.4 43.9 1.0
CB A:LEU745 4.5 42.7 1.0
N A:ASN741 4.5 42.7 1.0
C A:ASP739 4.5 41.1 1.0
N A:ARG746 4.5 39.6 1.0
CB A:ASP743 4.6 40.0 1.0
CB A:ASN741 4.6 39.9 1.0
N A:TYR742 4.7 43.4 1.0
OE2 A:GLU751 4.8 57.4 1.0
CA A:ARG746 4.8 41.1 1.0
N A:TYR740 4.8 42.6 1.0
C A:ASN741 4.8 45.6 1.0
CA A:ASP743 4.8 39.3 1.0
N A:GLY744 4.8 42.0 1.0
CA A:ASN741 4.8 42.7 1.0
N A:ASP739 5.0 41.2 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: Sat Feb 8 15:33:32 2025

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