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Calcium in PDB 7g6b: Crystal Structure of Rat Autotaxin in Complex with 6-Chloro-9-[2- (Oxan-2-Yloxy)Ethyl]-3,4-Dihydro-2H-Pyrido[3,4-B]Indol-1-One, I.E. Smiles C1(CCC2C(C1)C1=C(N2CCO[C@H]2OCCCC2)C(=O)NCC1)Cl with IC50=4.25663 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 6-Chloro-9-[2- (Oxan-2-Yloxy)Ethyl]-3,4-Dihydro-2H-Pyrido[3,4-B]Indol-1-One, I.E. Smiles C1(CCC2C(C1)C1=C(N2CCO[C@H]2OCCCC2)C(=O)NCC1)Cl with IC50=4.25663 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 6-Chloro-9-[2- (Oxan-2-Yloxy)Ethyl]-3,4-Dihydro-2H-Pyrido[3,4-B]Indol-1-One, I.E. Smiles C1(CCC2C(C1)C1=C(N2CCO[C@H]2OCCCC2)C(=O)NCC1)Cl with IC50=4.25663 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 6-Chloro-9-[2- (Oxan-2-Yloxy)Ethyl]-3,4-Dihydro-2H-Pyrido[3,4-B]Indol-1-One, I.E. Smiles C1(CCC2C(C1)C1=C(N2CCO[C@H]2OCCCC2)C(=O)NCC1)Cl with IC50=4.25663 Microm, PDB code: 7g6b was solved by M.Stihle, J.Benz, D.Hunziker, K.Koyama, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.92 / 1.61
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.017, 91.832, 119.256, 90, 90, 90
R / Rfree (%) 18.7 / 21.4

Other elements in 7g6b:

The structure of Crystal Structure of Rat Autotaxin in Complex with 6-Chloro-9-[2- (Oxan-2-Yloxy)Ethyl]-3,4-Dihydro-2H-Pyrido[3,4-B]Indol-1-One, I.E. Smiles C1(CCC2C(C1)C1=C(N2CCO[C@H]2OCCCC2)C(=O)NCC1)Cl with IC50=4.25663 Microm also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 6-Chloro-9-[2- (Oxan-2-Yloxy)Ethyl]-3,4-Dihydro-2H-Pyrido[3,4-B]Indol-1-One, I.E. Smiles C1(CCC2C(C1)C1=C(N2CCO[C@H]2OCCCC2)C(=O)NCC1)Cl with IC50=4.25663 Microm (pdb code 7g6b). 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 6-Chloro-9-[2- (Oxan-2-Yloxy)Ethyl]-3,4-Dihydro-2H-Pyrido[3,4-B]Indol-1-One, I.E. Smiles C1(CCC2C(C1)C1=C(N2CCO[C@H]2OCCCC2)C(=O)NCC1)Cl with IC50=4.25663 Microm, PDB code: 7g6b:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g6b

Go back to Calcium Binding Sites List in 7g6b
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 6-Chloro-9-[2- (Oxan-2-Yloxy)Ethyl]-3,4-Dihydro-2H-Pyrido[3,4-B]Indol-1-One, I.E. Smiles C1(CCC2C(C1)C1=C(N2CCO[C@H]2OCCCC2)C(=O)NCC1)Cl with IC50=4.25663 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 6-Chloro-9-[2- (Oxan-2-Yloxy)Ethyl]-3,4-Dihydro-2H-Pyrido[3,4-B]Indol-1-One, I.E. Smiles C1(CCC2C(C1)C1=C(N2CCO[C@H]2OCCCC2)C(=O)NCC1)Cl with IC50=4.25663 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:25.0
occ:1.00
 OD1 A:ASP171 1.8 22.4 1.0
OG1 A:THR209 2.0 18.6 1.0
NE2 A:HIS359 2.1 13.6 1.0
OD2 A:ASP358 2.2 16.3 1.0
CG A:ASP171 2.8 23.3 1.0
CE1 A:HIS359 2.9 14.6 1.0
CB A:THR209 3.0 17.0 1.0
CG A:ASP358 3.0 16.1 1.0
CD2 A:HIS359 3.0 14.6 1.0
CG2 A:THR209 3.2 19.1 1.0
OD1 A:ASP358 3.3 14.7 1.0
OD2 A:ASP171 3.3 31.4 1.0
CA A:THR209 3.4 14.6 1.0
O A:HOH1003 3.8 33.1 1.0
ND1 A:HIS359 4.0 14.6 1.0
N A:THR209 4.0 12.9 1.0
CB A:ASP171 4.0 18.1 1.0
OD2 A:ASP311 4.0 17.0 1.0
N A:GLY172 4.1 13.7 1.0
CG A:HIS359 4.1 13.6 1.0
CA A:ASP171 4.2 15.5 1.0
O1 A:SO4906 4.3 31.0 1.0
CB A:ASP358 4.3 15.3 1.0
CE1 A:HIS474 4.4 14.5 1.0
CG A:ASP311 4.4 16.3 1.0
O3 A:SO4906 4.5 27.7 1.0
C A:ASP171 4.5 14.6 1.0
ZN A:ZN907 4.5 16.8 1.0
NE2 A:HIS474 4.7 14.2 1.0
C A:THR209 4.7 14.1 1.0
CB A:ASP311 4.8 14.9 1.0
C A:LYS208 4.8 13.1 1.0
OD1 A:ASP311 4.9 19.7 1.0
CA A:GLY172 4.9 13.5 1.0

Calcium binding site 2 out of 2 in 7g6b

Go back to Calcium Binding Sites List in 7g6b
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 6-Chloro-9-[2- (Oxan-2-Yloxy)Ethyl]-3,4-Dihydro-2H-Pyrido[3,4-B]Indol-1-One, I.E. Smiles C1(CCC2C(C1)C1=C(N2CCO[C@H]2OCCCC2)C(=O)NCC1)Cl with IC50=4.25663 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 6-Chloro-9-[2- (Oxan-2-Yloxy)Ethyl]-3,4-Dihydro-2H-Pyrido[3,4-B]Indol-1-One, I.E. Smiles C1(CCC2C(C1)C1=C(N2CCO[C@H]2OCCCC2)C(=O)NCC1)Cl with IC50=4.25663 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca909

b:14.3
occ:1.00
 O A:LEU745 2.3 14.3 1.0
OD1 A:ASP747 2.3 16.0 1.0
O A:HOH1407 2.3 19.9 1.0
OD1 A:ASP739 2.3 13.7 1.0
OD1 A:ASN741 2.3 17.4 1.0
OD1 A:ASP743 2.3 16.4 1.0
CG A:ASP743 3.3 17.4 1.0
CG A:ASN741 3.4 18.6 1.0
C A:LEU745 3.4 13.4 1.0
CG A:ASP739 3.5 13.6 1.0
CG A:ASP747 3.5 16.0 1.0
OD2 A:ASP743 3.7 19.1 1.0
ND2 A:ASN741 3.9 21.9 1.0
N A:ASP747 3.9 13.4 1.0
CA A:ASP739 4.0 12.5 1.0
C A:ARG746 4.0 15.1 1.0
N A:LEU745 4.1 13.2 1.0
CA A:ASP747 4.1 14.1 1.0
CB A:ASP739 4.2 12.6 1.0
O A:ARG746 4.2 14.8 1.0
CA A:LEU745 4.2 13.6 1.0
N A:ASP743 4.3 14.8 1.0
OD2 A:ASP739 4.4 14.2 1.0
OD2 A:ASP747 4.4 17.0 1.0
N A:ASN741 4.4 15.4 1.0
CB A:ASP747 4.4 14.3 1.0
N A:ARG746 4.5 14.4 1.0
C A:ASP739 4.5 13.3 1.0
CB A:LEU745 4.5 14.2 1.0
O A:PHE738 4.5 13.6 1.0
CB A:ASP743 4.6 16.1 1.0
OE2 A:GLU751 4.6 30.0 1.0
CB A:ASN741 4.7 16.4 1.0
N A:TYR740 4.7 13.2 1.0
CA A:ARG746 4.7 14.3 1.0
N A:TYR742 4.8 15.1 1.0
O A:HOH1409 4.8 29.5 1.0
CA A:ASP743 4.8 15.7 1.0
CA A:ASN741 4.8 15.8 1.0
N A:GLY744 4.9 14.7 1.0
C A:ASN741 4.9 16.2 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 15:55:33 2025

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