Atomistry » Sodium » PDB 7g49-7g5t » 7g5f
Atomistry »
  Sodium »
    PDB 7g49-7g5t »
      7g5f »

Sodium in PDB 7g5f: Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[4-(Cyclopropylmethoxy)Naphthalene-2- 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)C1CC(C2C(C1)CCCC2)OCC1CC1 with IC50=0.00985223 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[4-(Cyclopropylmethoxy)Naphthalene-2- 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)C1CC(C2C(C1)CCCC2)OCC1CC1 with IC50=0.00985223 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[4-(Cyclopropylmethoxy)Naphthalene-2- 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)C1CC(C2C(C1)CCCC2)OCC1CC1 with IC50=0.00985223 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-[4-(Cyclopropylmethoxy)Naphthalene-2- 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)C1CC(C2C(C1)CCCC2)OCC1CC1 with IC50=0.00985223 Microm, PDB code: 7g5f 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) 45.98 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.078, 91.953, 120.1, 90, 90, 90
R / Rfree (%) 21.5 / 27

Other elements in 7g5f:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[4-(Cyclopropylmethoxy)Naphthalene-2- 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)C1CC(C2C(C1)CCCC2)OCC1CC1 with IC50=0.00985223 Microm also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 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 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[4-(Cyclopropylmethoxy)Naphthalene-2- 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)C1CC(C2C(C1)CCCC2)OCC1CC1 with IC50=0.00985223 Microm (pdb code 7g5f). 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 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[4-(Cyclopropylmethoxy)Naphthalene-2- 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)C1CC(C2C(C1)CCCC2)OCC1CC1 with IC50=0.00985223 Microm, PDB code: 7g5f:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g5f

Go back to Sodium Binding Sites List in 7g5f
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[4-(Cyclopropylmethoxy)Naphthalene-2- 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)C1CC(C2C(C1)CCCC2)OCC1CC1 with IC50=0.00985223 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-[4-(Cyclopropylmethoxy)Naphthalene-2- 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)C1CC(C2C(C1)CCCC2)OCC1CC1 with IC50=0.00985223 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na904

b:30.7
occ:1.00
 OG A:SER807 2.2 26.7 1.0
O A:SER804 2.4 21.9 1.0
O A:HOH1208 2.5 25.7 1.0
O A:HOH1225 2.7 37.7 1.0
O A:HOH1237 2.8 24.4 1.0
O A:ASN801 3.0 20.3 1.0
CB A:SER807 3.4 21.9 1.0
C A:SER804 3.6 26.1 1.0
C A:ASN801 3.7 20.0 1.0
N A:SER807 4.0 25.6 1.0
CA A:ASP802 4.0 22.4 1.0
CA A:CYS805 4.1 25.0 1.0
C A:CYS805 4.2 23.9 1.0
N A:ASP802 4.2 19.2 1.0
CA A:SER807 4.2 26.4 1.0
O A:CYS805 4.2 20.0 1.0
N A:CYS805 4.3 22.3 1.0
CB A:ASN801 4.5 19.3 1.0
C A:ASP802 4.6 23.0 1.0
OD1 A:ASP802 4.6 27.0 1.0
O A:ASP802 4.6 23.2 1.0
CA A:SER804 4.6 23.6 1.0
CA A:ASN801 4.7 18.9 1.0
C A:SER807 4.7 25.2 1.0
N A:SER804 4.7 16.5 1.0
N A:ASN806 4.7 24.6 1.0
N A:SER808 4.8 27.6 1.0
O A:HOH1168 4.8 25.1 1.0
CB A:SER804 4.9 25.1 1.0

Sodium binding site 2 out of 2 in 7g5f

Go back to Sodium Binding Sites List in 7g5f
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[4-(Cyclopropylmethoxy)Naphthalene-2- 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)C1CC(C2C(C1)CCCC2)OCC1CC1 with IC50=0.00985223 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-[4-(Cyclopropylmethoxy)Naphthalene-2- 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)C1CC(C2C(C1)CCCC2)OCC1CC1 with IC50=0.00985223 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:42.8
occ:1.00
 O A:TYR669 3.0 30.7 1.0
O A:MET675 3.1 30.2 1.0
O A:ASP672 3.3 26.2 1.0
C A:MET675 4.1 24.2 1.0
C A:TYR669 4.1 28.2 1.0
C A:ASP672 4.5 25.2 1.0
CA A:SER676 4.6 20.7 1.0
O A:LYS673 4.7 33.1 1.0
CA A:LYS673 4.7 30.3 1.0
N A:SER676 4.7 23.0 1.0
C A:LYS673 4.7 25.6 1.0
O A:LYS670 4.8 33.0 1.0
CB A:SER676 4.8 17.8 1.0
CA A:LYS670 4.8 30.1 1.0
N A:LYS670 4.9 29.7 1.0
N A:MET675 5.0 23.1 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 23:22:55 2025

Last articles

Zn in 8XYO
Zn in 8VWB
Zn in 8VWC
Zn in 8VWA
Zn in 8VW9
Zn in 8VMI
Zn in 8UFX
Zn in 8UFW
Zn in 8TU8
Zn in 8TU7
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy