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Sodium in PDB 7g3s: Crystal Structure of Rat Autotaxin in Complex with 2-[(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)Amino]-6-(Oxetan-3-Yl)-7H-Pyrrolo[3,4- D]Pyrimidin-5-One, I.E. Smiles O=C1N(C2COC2)CC2NC(N[C@H]3CC4C(C3) Ccc(C4)Cl)NCC12 with IC50=0.150181 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)Amino]-6-(Oxetan-3-Yl)-7H-Pyrrolo[3,4- D]Pyrimidin-5-One, I.E. Smiles O=C1N(C2COC2)CC2NC(N[C@H]3CC4C(C3) Ccc(C4)Cl)NCC12 with IC50=0.150181 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)Amino]-6-(Oxetan-3-Yl)-7H-Pyrrolo[3,4- D]Pyrimidin-5-One, I.E. Smiles O=C1N(C2COC2)CC2NC(N[C@H]3CC4C(C3) Ccc(C4)Cl)NCC12 with IC50=0.150181 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)Amino]-6-(Oxetan-3-Yl)-7H-Pyrrolo[3,4- D]Pyrimidin-5-One, I.E. Smiles O=C1N(C2COC2)CC2NC(N[C@H]3CC4C(C3) Ccc(C4)Cl)NCC12 with IC50=0.150181 Microm, PDB code: 7g3s was solved by M.Stihle, J.Benz, D.Hunziker, E.Pinard, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.10 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.17, 92.208, 119.918, 90, 90, 90
R / Rfree (%) 16.9 / 22.4

Other elements in 7g3s:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)Amino]-6-(Oxetan-3-Yl)-7H-Pyrrolo[3,4- D]Pyrimidin-5-One, I.E. Smiles O=C1N(C2COC2)CC2NC(N[C@H]3CC4C(C3) Ccc(C4)Cl)NCC12 with IC50=0.150181 Microm also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 2-[(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)Amino]-6-(Oxetan-3-Yl)-7H-Pyrrolo[3,4- D]Pyrimidin-5-One, I.E. Smiles O=C1N(C2COC2)CC2NC(N[C@H]3CC4C(C3) Ccc(C4)Cl)NCC12 with IC50=0.150181 Microm (pdb code 7g3s). 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 2-[(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)Amino]-6-(Oxetan-3-Yl)-7H-Pyrrolo[3,4- D]Pyrimidin-5-One, I.E. Smiles O=C1N(C2COC2)CC2NC(N[C@H]3CC4C(C3) Ccc(C4)Cl)NCC12 with IC50=0.150181 Microm, PDB code: 7g3s:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g3s

Go back to Sodium Binding Sites List in 7g3s
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)Amino]-6-(Oxetan-3-Yl)-7H-Pyrrolo[3,4- D]Pyrimidin-5-One, I.E. Smiles O=C1N(C2COC2)CC2NC(N[C@H]3CC4C(C3) Ccc(C4)Cl)NCC12 with IC50=0.150181 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 2-[(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)Amino]-6-(Oxetan-3-Yl)-7H-Pyrrolo[3,4- D]Pyrimidin-5-One, I.E. Smiles O=C1N(C2COC2)CC2NC(N[C@H]3CC4C(C3) Ccc(C4)Cl)NCC12 with IC50=0.150181 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:41.7
occ:1.00
 O A:HOH1444 2.2 40.9 1.0
O A:SER804 2.5 23.6 1.0
O A:HOH1136 2.5 30.0 1.0
OG A:SER807 2.5 27.5 1.0
O A:HOH1085 2.7 35.1 1.0
O A:ASN801 2.8 23.0 1.0
C A:SER804 3.5 23.4 1.0
C A:ASN801 3.6 22.4 1.0
CB A:SER807 3.7 26.8 1.0
CA A:ASP802 3.9 24.8 1.0
N A:SER807 4.1 29.2 1.0
CA A:CYS805 4.1 27.7 1.0
N A:ASP802 4.1 23.3 1.0
C A:CYS805 4.2 28.1 1.0
O A:CYS805 4.2 28.9 1.0
N A:CYS805 4.2 24.5 1.0
O A:HOH1140 4.3 38.4 1.0
O A:ASP802 4.3 23.1 1.0
C A:ASP802 4.3 23.6 1.0
O A:HOH1195 4.4 32.5 1.0
CA A:SER807 4.4 29.6 1.0
CA A:SER804 4.6 22.0 1.0
N A:SER804 4.6 21.1 1.0
OD1 A:ASP802 4.6 29.9 1.0
CA A:ASN801 4.7 22.8 1.0
CB A:ASN801 4.7 21.7 1.0
N A:ASN806 4.8 29.6 1.0
CB A:SER804 5.0 22.8 1.0

Sodium binding site 2 out of 2 in 7g3s

Go back to Sodium Binding Sites List in 7g3s
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)Amino]-6-(Oxetan-3-Yl)-7H-Pyrrolo[3,4- D]Pyrimidin-5-One, I.E. Smiles O=C1N(C2COC2)CC2NC(N[C@H]3CC4C(C3) Ccc(C4)Cl)NCC12 with IC50=0.150181 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 2-[(5-Chloro-2,3- Dihydro-1H-Inden-2-Yl)Amino]-6-(Oxetan-3-Yl)-7H-Pyrrolo[3,4- D]Pyrimidin-5-One, I.E. Smiles O=C1N(C2COC2)CC2NC(N[C@H]3CC4C(C3) Ccc(C4)Cl)NCC12 with IC50=0.150181 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:16.0
occ:1.00
 O A:ASP672 2.3 26.7 1.0
O A:MET675 2.3 27.6 1.0
O A:TYR669 2.3 27.4 1.0
O A:HOH1321 2.4 25.1 1.0
O A:HOH1442 2.6 36.8 1.0
O A:HOH1445 2.6 32.1 1.0
C A:MET675 3.4 24.9 1.0
C A:ASP672 3.5 29.5 1.0
C A:TYR669 3.5 27.0 1.0
N A:MET675 4.2 27.4 1.0
N A:SER676 4.2 22.0 1.0
CA A:TYR669 4.3 26.4 1.0
N A:LYS673 4.3 29.4 1.0
CA A:SER676 4.3 21.5 1.0
CA A:LYS673 4.4 34.0 1.0
O A:HOH1462 4.4 53.9 1.0
CA A:MET675 4.4 24.1 1.0
O A:LYS670 4.4 32.5 1.0
C A:LYS673 4.4 33.3 1.0
CA A:ASP672 4.4 29.2 1.0
N A:LYS670 4.5 28.8 1.0
N A:ASP672 4.6 30.8 1.0
O A:LYS673 4.6 33.1 1.0
CB A:ASP672 4.6 28.0 1.0
C A:LYS670 4.6 31.3 1.0
CA A:LYS670 4.6 32.2 1.0
CB A:TYR669 4.7 27.6 1.0
N A:GLN674 4.8 31.7 1.0
CB A:SER676 4.9 20.7 1.0
C A:GLN674 4.9 30.7 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 23:15:11 2025

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