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Sodium 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
Calcium (Ca) 2 atoms
Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g2i

Go back to Sodium Binding Sites List in 7g2i
Sodium 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 Sodium with other atoms in the Na 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:Na909

b:22.4
occ:1.00
 OG A:SER807 2.3 23.3 1.0
O A:HOH1383 2.4 24.3 1.0
O A:HOH1503 2.4 29.4 1.0
O A:ASN801 2.4 18.5 1.0
O A:SER804 2.4 21.4 1.0
O A:HOH1314 2.6 26.2 1.0
C A:ASN801 3.3 19.3 1.0
CB A:SER807 3.4 23.1 1.0
C A:SER804 3.5 21.1 1.0
CA A:ASP802 3.9 20.5 1.0
N A:ASP802 3.9 20.2 1.0
N A:SER807 4.1 22.3 1.0
C A:ASP802 4.2 21.4 1.0
CB A:ASN801 4.3 20.3 1.0
CA A:CYS805 4.3 23.3 1.0
O A:ASP802 4.3 20.4 1.0
N A:CYS805 4.3 21.6 1.0
CA A:SER807 4.3 23.9 1.0
O A:HOH1109 4.3 34.0 1.0
N A:SER804 4.3 18.5 1.0
CA A:ASN801 4.3 19.3 1.0
CA A:SER804 4.3 19.2 1.0
C A:CYS805 4.4 25.1 1.0
O A:CYS805 4.6 25.9 1.0
CB A:SER804 4.6 19.9 1.0
O A:HOH1281 4.7 32.1 1.0
OD1 A:ASP802 4.7 27.7 1.0
O A:HOH1311 4.7 29.2 1.0
N A:ASN806 4.9 24.0 1.0

Sodium binding site 2 out of 2 in 7g2i

Go back to Sodium Binding Sites List in 7g2i
Sodium 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 Sodium with other atoms in the Na 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:Na911

b:23.4
occ:1.00
 O A:TYR669 2.3 26.9 1.0
O A:MET675 2.3 24.2 1.0
O A:ASP672 2.3 24.6 1.0
O A:HOH1414 2.4 30.9 1.0
O A:HOH1494 2.6 37.1 1.0
O A:HOH1512 2.7 41.4 1.0
C A:TYR669 3.4 27.5 1.0
C A:MET675 3.4 22.3 1.0
C A:ASP672 3.5 24.6 1.0
N A:MET675 4.0 22.6 1.0
CA A:TYR669 4.2 22.8 1.0
CA A:MET675 4.3 21.7 1.0
O A:LYS670 4.3 31.0 1.0
N A:SER676 4.3 19.2 1.0
CA A:LYS673 4.3 27.1 1.0
N A:LYS673 4.4 24.8 1.0
CA A:ASP672 4.4 22.7 1.0
N A:LYS670 4.4 26.9 1.0
C A:LYS673 4.4 27.3 1.0
N A:ASP672 4.4 25.1 1.0
CA A:SER676 4.5 19.6 1.0
O A:HOH1577 4.5 46.5 1.0
C A:LYS670 4.6 29.4 1.0
CB A:TYR669 4.6 23.3 1.0
CB A:ASP672 4.6 22.1 1.0
O A:LYS673 4.6 28.9 1.0
CA A:LYS670 4.6 31.4 1.0
O A:HOH1560 4.7 42.7 1.0
N A:GLN674 4.8 25.6 1.0
CB A:MET675 4.9 21.0 1.0
C A:GLN674 5.0 25.6 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 23:09:23 2025

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