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Sodium in PDB 7g4c: Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(1-Ethyl-4-Propan-2-Yloxyindole-6-Carbonyl)- 4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC2C(C(C1)Oc(C)C)C=CN2CC with IC50=0.0412147 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(1-Ethyl-4-Propan-2-Yloxyindole-6-Carbonyl)- 4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC2C(C(C1)Oc(C)C)C=CN2CC with IC50=0.0412147 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(1-Ethyl-4-Propan-2-Yloxyindole-6-Carbonyl)- 4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC2C(C(C1)Oc(C)C)C=CN2CC with IC50=0.0412147 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(1-Ethyl-4-Propan-2-Yloxyindole-6-Carbonyl)- 4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC2C(C(C1)Oc(C)C)C=CN2CC with IC50=0.0412147 Microm, PDB code: 7g4c 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) 45.84 / 1.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.835, 91.673, 118.797, 90, 90, 90
R / Rfree (%) 17.6 / 20.9

Other elements in 7g4c:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(1-Ethyl-4-Propan-2-Yloxyindole-6-Carbonyl)- 4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC2C(C(C1)Oc(C)C)C=CN2CC with IC50=0.0412147 Microm also contains other interesting chemical elements:

Calcium (Ca) 1 atom
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 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(1-Ethyl-4-Propan-2-Yloxyindole-6-Carbonyl)- 4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC2C(C(C1)Oc(C)C)C=CN2CC with IC50=0.0412147 Microm (pdb code 7g4c). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(1-Ethyl-4-Propan-2-Yloxyindole-6-Carbonyl)- 4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC2C(C(C1)Oc(C)C)C=CN2CC with IC50=0.0412147 Microm, PDB code: 7g4c:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 7g4c

Go back to Sodium Binding Sites List in 7g4c
Sodium binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(1-Ethyl-4-Propan-2-Yloxyindole-6-Carbonyl)- 4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC2C(C(C1)Oc(C)C)C=CN2CC with IC50=0.0412147 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 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(1-Ethyl-4-Propan-2-Yloxyindole-6-Carbonyl)- 4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC2C(C(C1)Oc(C)C)C=CN2CC with IC50=0.0412147 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:20.6
occ:1.00
 O A:SER804 2.3 17.9 1.0
OG A:SER807 2.4 19.4 1.0
O A:HOH1378 2.4 19.3 1.0
O A:ASN801 2.4 16.0 1.0
O A:HOH1502 2.4 25.7 1.0
O A:HOH1406 2.5 22.7 1.0
C A:ASN801 3.3 16.7 1.0
C A:SER804 3.4 16.7 1.0
CB A:SER807 3.4 18.5 1.0
CA A:ASP802 3.9 18.3 1.0
N A:ASP802 4.0 16.4 1.0
N A:SER807 4.1 18.2 1.0
C A:ASP802 4.2 16.4 1.0
CA A:CYS805 4.2 20.3 1.0
O A:ASP802 4.2 16.6 1.0
N A:CYS805 4.2 18.6 1.0
CB A:ASN801 4.3 16.1 1.0
N A:SER804 4.3 13.8 1.0
CA A:SER807 4.3 19.0 1.0
O A:HOH1080 4.3 29.7 1.0
CA A:SER804 4.3 13.8 1.0
CA A:ASN801 4.4 15.9 1.0
C A:CYS805 4.4 22.9 1.0
O A:CYS805 4.5 22.5 1.0
CB A:SER804 4.6 15.7 1.0
O A:HOH1228 4.7 28.8 1.0
OD1 A:ASP802 4.7 25.9 1.0
O A:HOH1355 4.9 23.6 1.0
N A:ASN806 4.9 21.9 1.0
N A:GLU803 5.0 13.5 1.0
C A:SER807 5.0 22.7 1.0

Sodium binding site 2 out of 3 in 7g4c

Go back to Sodium Binding Sites List in 7g4c
Sodium binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(1-Ethyl-4-Propan-2-Yloxyindole-6-Carbonyl)- 4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC2C(C(C1)Oc(C)C)C=CN2CC with IC50=0.0412147 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 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(1-Ethyl-4-Propan-2-Yloxyindole-6-Carbonyl)- 4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC2C(C(C1)Oc(C)C)C=CN2CC with IC50=0.0412147 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:21.3
occ:1.00
 O A:MET675 2.3 20.6 1.0
O A:TYR669 2.3 23.7 1.0
O A:ASP672 2.4 21.3 1.0
O A:HOH1436 2.4 28.7 1.0
O A:HOH1496 2.7 35.2 1.0
O A:HOH1491 2.8 40.2 1.0
C A:MET675 3.5 20.9 1.0
C A:TYR669 3.5 23.2 1.0
C A:ASP672 3.6 22.3 1.0
N A:MET675 4.0 19.8 1.0
CA A:TYR669 4.2 18.3 1.0
CA A:MET675 4.3 17.9 1.0
O A:LYS670 4.3 31.1 1.0
N A:SER676 4.4 15.8 1.0
CA A:LYS673 4.4 24.2 1.0
N A:ASP672 4.4 24.1 1.0
CA A:SER676 4.4 16.4 1.0
CA A:ASP672 4.5 22.0 1.0
C A:LYS673 4.5 24.3 1.0
N A:LYS670 4.5 22.3 1.0
N A:LYS673 4.5 23.0 1.0
O A:LYS673 4.6 25.2 1.0
C A:LYS670 4.6 27.6 1.0
CA A:LYS670 4.6 28.3 1.0
CB A:TYR669 4.6 19.3 1.0
CB A:ASP672 4.6 21.8 1.0
N A:GLN674 4.9 21.0 1.0
CB A:MET675 4.9 18.0 1.0
C A:GLN674 5.0 22.1 1.0

Sodium binding site 3 out of 3 in 7g4c

Go back to Sodium Binding Sites List in 7g4c
Sodium binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(1-Ethyl-4-Propan-2-Yloxyindole-6-Carbonyl)- 4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC2C(C(C1)Oc(C)C)C=CN2CC with IC50=0.0412147 Microm


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(1-Ethyl-4-Propan-2-Yloxyindole-6-Carbonyl)- 4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC2C(C(C1)Oc(C)C)C=CN2CC with IC50=0.0412147 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na909

b:42.0
occ:1.00
 O A:ASN650 2.3 25.1 1.0
O A:HOH1265 2.4 28.5 1.0
OG1 A:THR567 2.5 36.3 1.0
O A:HOH1498 2.5 33.2 1.0
O A:THR567 2.6 27.3 1.0
C A:ASN650 3.2 26.0 1.0
C A:THR567 3.3 32.1 1.0
N A:THR567 3.5 29.6 1.0
CB A:THR567 3.6 34.9 1.0
CA A:THR567 3.6 33.7 1.0
CB A:ASN650 3.8 32.9 1.0
N A:CYS651 4.0 23.8 1.0
O A:HOH1083 4.1 40.8 1.0
CA A:CYS651 4.1 21.5 1.0
CA A:ASN650 4.1 30.4 1.0
O A:HOH1460 4.3 36.3 1.0
N A:CYS568 4.3 28.6 1.0
N A:VAL652 4.3 17.4 1.0
C A:CYS651 4.6 19.5 1.0
C A:CYS566 4.7 33.6 1.0
CG2 A:THR567 4.7 38.2 1.0
CA A:CYS568 4.8 29.8 1.0
O A:HOH1260 4.9 36.2 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 23:18:33 2025

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