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Calcium in PDB 7g6q: Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-3-Nitro-N-Phenylbenzamide, I.E. Smiles C1CNC2C(C1)C(=CN2CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)NC1CCCCC1 with IC50=0.0309996 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-3-Nitro-N-Phenylbenzamide, I.E. Smiles C1CNC2C(C1)C(=CN2CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)NC1CCCCC1 with IC50=0.0309996 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-3-Nitro-N-Phenylbenzamide, I.E. Smiles C1CNC2C(C1)C(=CN2CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)NC1CCCCC1 with IC50=0.0309996 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-3-Nitro-N-Phenylbenzamide, I.E. Smiles C1CNC2C(C1)C(=CN2CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)NC1CCCCC1 with IC50=0.0309996 Microm, PDB code: 7g6q was solved by M.Stihle, J.Benz, D.Hunziker, E.Martin-Rainer, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.78 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.041, 91.659, 119.803, 90, 90, 90
R / Rfree (%) 19 / 23.6

Other elements in 7g6q:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-3-Nitro-N-Phenylbenzamide, I.E. Smiles C1CNC2C(C1)C(=CN2CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)NC1CCCCC1 with IC50=0.0309996 Microm also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-3-Nitro-N-Phenylbenzamide, I.E. Smiles C1CNC2C(C1)C(=CN2CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)NC1CCCCC1 with IC50=0.0309996 Microm (pdb code 7g6q). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-3-Nitro-N-Phenylbenzamide, I.E. Smiles C1CNC2C(C1)C(=CN2CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)NC1CCCCC1 with IC50=0.0309996 Microm, PDB code: 7g6q:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g6q

Go back to Calcium Binding Sites List in 7g6q
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-3-Nitro-N-Phenylbenzamide, I.E. Smiles C1CNC2C(C1)C(=CN2CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)NC1CCCCC1 with IC50=0.0309996 Microm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-3-Nitro-N-Phenylbenzamide, I.E. Smiles C1CNC2C(C1)C(=CN2CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)NC1CCCCC1 with IC50=0.0309996 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:47.4
occ:1.00
 OG1 A:THR209 1.9 25.1 1.0
OD1 A:ASP171 1.9 32.1 1.0
NE2 A:HIS359 2.2 21.7 1.0
OD2 A:ASP358 2.4 26.3 1.0
CG A:ASP171 2.8 31.3 1.0
CB A:THR209 2.9 23.6 1.0
CE1 A:HIS359 3.0 20.7 1.0
OD2 A:ASP171 3.1 40.5 1.0
CD2 A:HIS359 3.1 21.5 1.0
CG A:ASP358 3.2 24.8 1.0
CG2 A:THR209 3.2 23.7 1.0
CA A:THR209 3.3 24.3 1.0
O A:HOH1070 3.3 44.8 1.0
OD1 A:ASP358 3.4 22.6 1.0
N A:THR209 3.8 24.0 1.0
CB A:ASP171 4.1 27.7 1.0
ND1 A:HIS359 4.1 20.5 1.0
OD1 A:ASP311 4.2 28.4 1.0
CG A:HIS359 4.2 21.5 1.0
N A:GLY172 4.3 23.5 1.0
CE1 A:HIS474 4.3 21.1 1.0
CA A:ASP171 4.4 25.7 1.0
CG A:ASP311 4.4 27.8 1.0
NE2 A:HIS474 4.4 22.1 1.0
ZN A:ZN905 4.5 27.6 1.0
CB A:ASP358 4.5 23.4 1.0
C A:LYS208 4.6 25.6 1.0
C A:THR209 4.7 23.9 1.0
O A:HOH1359 4.7 32.7 1.0
C A:ASP171 4.7 25.4 1.0
OD2 A:ASP311 4.8 30.6 1.0
CB A:ASP311 4.8 27.4 1.0
OH A:TYR306 4.9 34.4 1.0

Calcium binding site 2 out of 2 in 7g6q

Go back to Calcium Binding Sites List in 7g6q
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-3-Nitro-N-Phenylbenzamide, I.E. Smiles C1CNC2C(C1)C(=CN2CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)NC1CCCCC1 with IC50=0.0309996 Microm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-3-Nitro-N-Phenylbenzamide, I.E. Smiles C1CNC2C(C1)C(=CN2CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)NC1CCCCC1 with IC50=0.0309996 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:23.1
occ:1.00
 OD1 A:ASP747 2.2 22.6 1.0
O A:LEU745 2.3 21.8 1.0
OD1 A:ASN741 2.3 24.5 1.0
OD1 A:ASP743 2.3 24.9 1.0
OD1 A:ASP739 2.3 23.5 1.0
O A:HOH1342 2.4 24.2 1.0
CG A:ASP743 3.3 25.9 1.0
CG A:ASN741 3.4 25.4 1.0
C A:LEU745 3.5 23.5 1.0
CG A:ASP747 3.5 24.8 1.0
CG A:ASP739 3.5 23.6 1.0
OD2 A:ASP743 3.7 26.6 1.0
ND2 A:ASN741 3.9 23.9 1.0
N A:ASP747 3.9 21.2 1.0
CA A:ASP739 4.0 21.4 1.0
C A:ARG746 4.0 23.2 1.0
N A:LEU745 4.1 20.4 1.0
CA A:ASP747 4.2 23.8 1.0
O A:ARG746 4.2 23.6 1.0
CA A:LEU745 4.2 21.3 1.0
CB A:ASP739 4.2 21.6 1.0
OD2 A:ASP747 4.3 25.5 1.0
N A:ASP743 4.3 21.9 1.0
CB A:LEU745 4.4 23.4 1.0
CB A:ASP747 4.4 22.0 1.0
OD2 A:ASP739 4.4 22.9 1.0
O A:PHE738 4.4 18.6 1.0
N A:ASN741 4.4 23.7 1.0
C A:ASP739 4.5 21.2 1.0
N A:ARG746 4.5 23.1 1.0
OE2 A:GLU751 4.6 44.3 1.0
CB A:ASP743 4.6 22.8 1.0
CA A:ARG746 4.7 23.1 1.0
CB A:ASN741 4.7 23.5 1.0
N A:TYR740 4.8 23.3 1.0
N A:TYR742 4.8 23.6 1.0
CA A:ASP743 4.9 22.9 1.0
N A:GLY744 4.9 22.1 1.0
C A:ASN741 4.9 25.9 1.0
CA A:ASN741 4.9 25.1 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 15:56:56 2025

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