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Calcium in PDB 7g2i: Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 Microm, PDB code: 7g2i 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) 48.39 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.539, 91.509, 118.741, 90, 90, 90
R / Rfree (%) 15.9 / 18.5

Other elements in 7g2i:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 Microm also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Sodium (Na) 2 atoms
Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 Microm (pdb code 7g2i). 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-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 Microm, PDB code: 7g2i:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g2i

Go back to Calcium Binding Sites List in 7g2i
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 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-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:21.6
occ:1.00
 OD1 A:ASP171 1.9 20.6 1.0
OG1 A:THR209 1.9 18.9 1.0
NE2 A:HIS359 2.0 15.7 1.0
OD2 A:ASP358 2.2 19.0 1.0
CG A:ASP171 2.7 21.9 1.0
CB A:THR209 2.9 18.1 1.0
OD2 A:ASP171 2.9 30.5 1.0
CD2 A:HIS359 3.0 15.4 1.0
CE1 A:HIS359 3.0 16.6 1.0
CG A:ASP358 3.0 17.5 1.0
CG2 A:THR209 3.2 20.7 1.0
OD1 A:ASP358 3.3 14.0 1.0
CA A:THR209 3.3 15.7 1.0
O1 A:SO4905 3.8 51.1 1.0
O A:HOH1022 3.9 35.7 1.0
N A:THR209 3.9 15.3 1.0
CB A:ASP171 4.0 17.1 1.0
ND1 A:HIS359 4.0 16.2 1.0
CG A:HIS359 4.0 14.6 1.0
OD1 A:ASP311 4.1 19.9 1.0
N A:GLY172 4.1 14.8 1.0
CA A:ASP171 4.3 16.3 1.0
CB A:ASP358 4.3 14.3 1.0
CE1 A:HIS474 4.4 17.9 1.0
O A:HOH1012 4.4 26.0 1.0
CG A:ASP311 4.4 18.8 1.0
C A:ASP171 4.6 16.2 1.0
ZN A:ZN908 4.6 18.7 1.0
C A:THR209 4.7 16.0 1.0
NE2 A:HIS474 4.7 16.9 1.0
C A:LYS208 4.7 16.5 1.0
CB A:ASP311 4.8 16.7 1.0
CA A:GLY172 5.0 15.2 1.0

Calcium binding site 2 out of 2 in 7g2i

Go back to Calcium Binding Sites List in 7g2i
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 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-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca910

b:14.5
occ:1.00
 OD1 A:ASP747 2.3 16.7 1.0
OD1 A:ASN741 2.3 17.1 1.0
O A:LEU745 2.3 14.6 1.0
OD1 A:ASP739 2.3 14.4 1.0
O A:HOH1481 2.3 20.5 1.0
OD1 A:ASP743 2.4 15.5 1.0
CG A:ASP743 3.3 16.8 1.0
CG A:ASN741 3.3 20.2 1.0
CG A:ASP739 3.4 14.7 1.0
C A:LEU745 3.5 13.3 1.0
CG A:ASP747 3.5 15.0 1.0
OD2 A:ASP743 3.7 18.5 1.0
ND2 A:ASN741 3.8 23.8 1.0
N A:ASP747 3.9 14.4 1.0
CA A:ASP739 4.0 13.6 1.0
C A:ARG746 4.1 15.5 1.0
N A:LEU745 4.1 13.0 1.0
CA A:ASP747 4.1 14.0 1.0
CB A:ASP739 4.2 13.9 1.0
O A:ARG746 4.2 16.0 1.0
CA A:LEU745 4.2 14.4 1.0
N A:ASP743 4.3 15.0 1.0
OD2 A:ASP739 4.4 13.8 1.0
OD2 A:ASP747 4.4 16.6 1.0
CB A:ASP747 4.4 14.8 1.0
O A:PHE738 4.4 14.6 1.0
C A:ASP739 4.5 14.1 1.0
CB A:LEU745 4.5 15.0 1.0
N A:ASN741 4.5 14.8 1.0
N A:ARG746 4.5 14.3 1.0
CB A:ASP743 4.5 15.6 1.0
CB A:ASN741 4.6 16.8 1.0
O A:HOH1396 4.6 29.6 1.0
OE2 A:GLU751 4.7 26.7 1.0
N A:TYR740 4.7 14.8 1.0
CA A:ARG746 4.7 14.9 1.0
N A:TYR742 4.8 16.2 1.0
CA A:ASP743 4.8 15.7 1.0
CA A:ASN741 4.9 15.9 1.0
C A:ASN741 4.9 16.5 1.0
N A:GLY744 4.9 14.5 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 15:33:41 2025

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