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Sodium in PDB 7g4w: Crystal Structure of Rat Autotaxin in Complex with (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]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)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]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)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]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)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]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)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 Microm, PDB code: 7g4w 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) 45.79 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.98, 91.582, 119.383, 90, 90, 90
R / Rfree (%) 19.3 / 23.4

Other elements in 7g4w:

The structure of Crystal Structure of Rat Autotaxin in Complex with (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]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)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 Microm also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]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)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 Microm (pdb code 7g4w). 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 (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]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)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 Microm, PDB code: 7g4w:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 7g4w

Go back to Sodium Binding Sites List in 7g4w
Sodium binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]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)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 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 (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]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)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na903

b:31.7
occ:1.00
 OG A:SER807 2.2 27.6 1.0
O A:SER804 2.3 27.3 1.0
O A:HOH1200 2.4 29.1 1.0
O A:HOH1379 2.4 36.2 1.0
O A:HOH1326 2.5 32.1 1.0
O A:ASN801 2.5 27.1 1.0
C A:ASN801 3.4 26.0 1.0
CB A:SER807 3.4 27.5 1.0
C A:SER804 3.4 26.6 1.0
CA A:ASP802 3.9 28.6 1.0
N A:SER807 4.0 31.5 1.0
N A:ASP802 4.0 25.3 1.0
O A:ASP802 4.2 28.8 1.0
C A:ASP802 4.2 27.6 1.0
O A:HOH1106 4.2 42.5 1.0
CA A:CYS805 4.2 30.2 1.0
CA A:SER807 4.2 32.2 1.0
N A:CYS805 4.2 28.5 1.0
N A:SER804 4.3 23.6 1.0
CB A:ASN801 4.3 25.3 1.0
C A:CYS805 4.3 31.7 1.0
CA A:SER804 4.3 24.6 1.0
CA A:ASN801 4.4 25.4 1.0
O A:CYS805 4.5 29.8 1.0
CB A:SER804 4.7 26.2 1.0
O A:HOH1107 4.8 33.3 1.0
OD1 A:ASP802 4.8 35.0 1.0
N A:ASN806 4.8 31.8 1.0
O A:HOH1128 4.8 38.3 1.0
C A:SER807 5.0 33.1 1.0
N A:GLU803 5.0 26.4 1.0

Sodium binding site 2 out of 3 in 7g4w

Go back to Sodium Binding Sites List in 7g4w
Sodium binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]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)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 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 (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]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)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na904

b:40.2
occ:1.00
 O A:HOH1369 2.3 40.8 1.0
O A:HOH1236 2.4 40.0 1.0
O A:CYS568 2.5 43.5 1.0
OD1 A:ASP570 2.6 57.1 1.0
C A:CYS568 3.6 46.0 1.0
CE A:LYS571 3.7 80.0 1.0
CG A:ASP570 3.8 59.2 1.0
N A:CYS568 3.9 38.9 1.0
NZ A:LYS571 4.0 80.0 1.0
CD A:LYS571 4.1 80.0 1.0
CG A:LYS571 4.1 80.0 1.0
CA A:CYS568 4.1 42.1 1.0
N A:ASP570 4.2 60.3 1.0
CB A:CYS568 4.3 37.1 1.0
OD2 A:ASP570 4.4 52.4 1.0
O A:HOH1069 4.6 38.0 1.0
N A:LYS571 4.7 76.2 1.0
N A:ASP569 4.7 50.1 1.0
CB A:ASP570 4.8 62.9 1.0
CA A:ASP570 4.9 65.6 1.0
NE2 A:GLN559 5.0 52.4 1.0

Sodium binding site 3 out of 3 in 7g4w

Go back to Sodium Binding Sites List in 7g4w
Sodium binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]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)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 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 (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]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)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:46.9
occ:1.00
 O A:ASN650 2.3 37.8 1.0
O A:HOH1234 2.3 38.9 1.0
O A:THR567 2.5 38.4 1.0
OG1 A:THR567 2.6 39.4 1.0
O A:HOH1376 2.6 40.3 1.0
O A:HOH1366 2.7 50.4 1.0
C A:ASN650 3.1 37.4 1.0
C A:THR567 3.2 41.0 1.0
N A:THR567 3.5 39.4 1.0
CA A:THR567 3.7 40.9 1.0
CB A:THR567 3.7 42.8 1.0
N A:CYS651 3.8 33.4 1.0
CA A:CYS651 3.8 33.5 1.0
CB A:ASN650 3.9 46.9 1.0
CA A:ASN650 4.1 43.2 1.0
N A:VAL652 4.1 25.9 1.0
O A:HOH1362 4.2 42.8 1.0
N A:CYS568 4.3 38.9 1.0
C A:CYS651 4.3 29.4 1.0
CA A:CYS568 4.7 42.1 1.0
CG2 A:THR567 4.8 41.2 1.0
C A:CYS566 4.8 41.6 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 23:18:33 2025

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