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Calcium in PDB 7g2y: Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm, PDB code: 7g2y 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) 48.68 / 1.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.882, 91.634, 119.543, 90, 90, 90
R / Rfree (%) 17.9 / 22

Other elements in 7g2y:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom
Potassium (K) 1 atom
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm (pdb code 7g2y). 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 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm, PDB code: 7g2y:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g2y

Go back to Calcium Binding Sites List in 7g2y
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 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 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:22.5
occ:1.00
 OG1 A:THR209 1.9 19.9 1.0
OD1 A:ASP171 1.9 23.8 1.0
NE2 A:HIS359 2.1 19.9 1.0
OD2 A:ASP358 2.2 22.4 1.0
CG A:ASP171 2.6 25.7 1.0
OD2 A:ASP171 2.7 31.2 1.0
CE1 A:HIS359 2.9 18.7 1.0
CB A:THR209 2.9 20.8 1.0
CG A:ASP358 3.0 19.1 1.0
CD2 A:HIS359 3.1 18.5 1.0
OD1 A:ASP358 3.3 17.3 1.0
CA A:THR209 3.3 18.7 1.0
CG2 A:THR209 3.4 22.4 1.0
N38 A:XH0904 3.5 34.4 1.0
N A:THR209 3.7 18.6 1.0
CB A:ASP171 4.0 21.7 1.0
ND1 A:HIS359 4.0 19.9 1.0
CG A:HIS359 4.1 18.9 1.0
N A:GLY172 4.2 18.3 1.0
OD1 A:ASP311 4.3 22.5 1.0
O39 A:XH0904 4.3 27.2 1.0
CA A:ASP171 4.3 21.0 1.0
CB A:ASP358 4.3 18.5 1.0
S36 A:XH0904 4.5 40.1 1.0
CG A:ASP311 4.5 22.7 1.0
CE1 A:HIS474 4.5 18.5 1.0
C A:ASP171 4.6 19.5 1.0
C A:LYS208 4.6 20.3 1.0
ZN A:ZN906 4.6 20.3 1.0
C A:THR209 4.7 18.2 1.0
NE2 A:HIS474 4.7 19.2 1.0
CB A:ASP311 4.9 22.5 1.0
C35 A:XH0904 4.9 45.8 1.0
OD2 A:ASP311 4.9 24.4 1.0
OH A:TYR306 5.0 27.9 1.0

Calcium binding site 2 out of 2 in 7g2y

Go back to Calcium Binding Sites List in 7g2y
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 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 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:18.1
occ:1.00
 OD1 A:ASP747 2.2 18.0 1.0
OD1 A:ASN741 2.3 19.6 1.0
O A:LEU745 2.3 18.5 1.0
OD1 A:ASP739 2.3 17.7 1.0
OD1 A:ASP743 2.3 19.5 1.0
O A:HOH1432 2.3 22.9 1.0
CG A:ASP743 3.3 20.1 1.0
CG A:ASN741 3.4 22.3 1.0
CG A:ASP739 3.5 16.5 1.0
CG A:ASP747 3.5 16.3 1.0
C A:LEU745 3.5 16.9 1.0
OD2 A:ASP743 3.7 21.3 1.0
ND2 A:ASN741 3.8 22.8 1.0
N A:ASP747 3.9 16.1 1.0
CA A:ASP739 4.0 16.2 1.0
C A:ARG746 4.1 19.7 1.0
N A:LEU745 4.1 16.2 1.0
CA A:ASP747 4.2 17.0 1.0
CB A:ASP739 4.2 16.2 1.0
O A:ARG746 4.2 16.6 1.0
CA A:LEU745 4.3 17.0 1.0
OD2 A:ASP747 4.3 18.6 1.0
N A:ASP743 4.3 16.9 1.0
OD2 A:ASP739 4.4 17.5 1.0
CB A:ASP747 4.4 16.3 1.0
O A:PHE738 4.5 16.0 1.0
N A:ARG746 4.5 18.3 1.0
CB A:LEU745 4.5 17.6 1.0
N A:ASN741 4.5 19.1 1.0
C A:ASP739 4.5 17.1 1.0
CB A:ASP743 4.5 19.8 1.0
OE2 A:GLU751 4.6 41.6 1.0
CB A:ASN741 4.7 20.2 1.0
N A:TYR740 4.7 17.8 1.0
CA A:ARG746 4.7 16.5 1.0
N A:TYR742 4.8 18.5 1.0
O A:HOH1419 4.8 35.9 1.0
CA A:ASP743 4.8 19.3 1.0
N A:GLY744 4.9 18.3 1.0
C A:ASN741 4.9 19.5 1.0
CA A:ASN741 4.9 19.1 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 15:35:08 2025

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