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Fluorine in PDB 6xdd: Crystal Structure of IRE1 in Complex with G-3053

Enzymatic activity of Crystal Structure of IRE1 in Complex with G-3053

All present enzymatic activity of Crystal Structure of IRE1 in Complex with G-3053:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of IRE1 in Complex with G-3053, PDB code: 6xdd was solved by H.Ackerly-Wallweber, W.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.62 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.201, 156.816, 157.766, 90, 90, 90
R / Rfree (%) 19.8 / 23.8

Other elements in 6xdd:

The structure of Crystal Structure of IRE1 in Complex with G-3053 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of IRE1 in Complex with G-3053 (pdb code 6xdd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of IRE1 in Complex with G-3053, PDB code: 6xdd:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6xdd

Go back to Fluorine Binding Sites List in 6xdd
Fluorine binding site 1 out of 6 in the Crystal Structure of IRE1 in Complex with G-3053


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of IRE1 in Complex with G-3053 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:61.8
occ:1.00
 F41 A:N971001 0.0 61.8 1.0
C13 A:N971001 1.3 61.5 1.0
C14 A:N971001 2.4 58.3 1.0
C12 A:N971001 2.4 64.9 1.0
O21 A:N971001 2.7 65.3 1.0
N11 A:N971001 2.7 67.5 1.0
N19 A:N971001 2.8 60.1 1.0
C20 A:N971001 3.0 58.5 1.0
OD2 A:ASP711 3.0 73.6 1.0
CG A:ASP711 3.3 70.0 1.0
N A:ASP711 3.5 48.2 1.0
C15 A:N971001 3.6 54.6 1.0
C17 A:N971001 3.7 60.2 1.0
CA A:ASP711 3.7 49.4 1.0
OD1 A:ASP711 3.7 79.5 1.0
S8 A:N971001 3.9 72.2 1.0
O10 A:N971001 4.0 78.7 1.0
NZ A:LYS599 4.0 73.0 1.0
OG A:SER710 4.0 57.6 1.0
CB A:ASP711 4.1 59.3 1.0
CB A:SER710 4.1 50.4 1.0
C16 A:N971001 4.1 55.3 1.0
C22 A:N971001 4.2 58.3 1.0
O9 A:N971001 4.3 78.6 1.0
CD1 A:ILE642 4.4 59.0 1.0
C A:SER710 4.6 45.8 1.0
CD A:LYS599 4.7 71.0 1.0
F7 A:N971001 4.9 71.3 1.0
CE A:LYS599 5.0 73.2 1.0

Fluorine binding site 2 out of 6 in 6xdd

Go back to Fluorine Binding Sites List in 6xdd
Fluorine binding site 2 out of 6 in the Crystal Structure of IRE1 in Complex with G-3053


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of IRE1 in Complex with G-3053 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:81.3
occ:1.00
 F42 A:N971001 0.0 81.3 1.0
C2 A:N971001 1.4 76.8 1.0
C3 A:N971001 2.4 73.8 1.0
C1 A:N971001 2.4 74.9 1.0
CA A:ALA609 3.1 75.3 1.0
CB A:ALA609 3.3 74.7 1.0
C4 A:N971001 3.6 73.3 1.0
C6 A:N971001 3.6 69.9 1.0
CD1 A:ILE601 3.7 71.3 1.0
N A:ALA609 3.9 85.3 1.0
CD1 A:ILE640 4.1 57.7 1.0
C5 A:N971001 4.1 70.1 1.0
C A:ALA609 4.2 69.4 1.0
O A:ALA609 4.2 72.0 1.0
C A:PHE608 4.5 94.0 1.0
CB A:GLU612 4.7 63.6 1.0
CG A:GLU612 4.7 66.6 1.0
O A:PHE608 4.8 89.7 1.0
CA A:GLY713 4.9 53.3 1.0
O A:CYS605 4.9 131.4 1.0

Fluorine binding site 3 out of 6 in 6xdd

Go back to Fluorine Binding Sites List in 6xdd
Fluorine binding site 3 out of 6 in the Crystal Structure of IRE1 in Complex with G-3053


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of IRE1 in Complex with G-3053 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:71.3
occ:1.00
 F7 A:N971001 0.0 71.3 1.0
C5 A:N971001 1.3 70.1 1.0
C6 A:N971001 2.4 69.9 1.0
C4 A:N971001 2.4 73.3 1.0
N11 A:N971001 2.4 67.5 1.0
S8 A:N971001 2.9 72.2 1.0
C12 A:N971001 3.2 64.9 1.0
N A:PHE712 3.3 50.5 1.0
C17 A:N971001 3.4 60.2 1.0
O9 A:N971001 3.5 78.6 1.0
C1 A:N971001 3.6 74.9 1.0
C3 A:N971001 3.6 73.8 1.0
CB A:PHE712 3.7 56.0 1.0
CA A:PHE712 3.8 52.5 1.0
N A:GLY713 3.9 55.5 1.0
C A:PHE712 3.9 53.8 1.0
CD2 A:LEU616 4.1 49.9 1.0
O10 A:N971001 4.1 78.7 1.0
C2 A:N971001 4.1 76.8 1.0
C A:ASP711 4.3 49.5 1.0
CA A:ASP711 4.4 49.4 1.0
C13 A:N971001 4.5 61.5 1.0
O A:PHE712 4.6 53.2 1.0
CA A:GLY713 4.6 53.3 1.0
C16 A:N971001 4.7 55.3 1.0
N A:ASP711 4.7 48.2 1.0
CG A:PHE712 4.8 54.7 1.0
CD2 A:PHE712 4.9 52.2 1.0
F41 A:N971001 4.9 61.8 1.0

Fluorine binding site 4 out of 6 in 6xdd

Go back to Fluorine Binding Sites List in 6xdd
Fluorine binding site 4 out of 6 in the Crystal Structure of IRE1 in Complex with G-3053


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of IRE1 in Complex with G-3053 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:64.6
occ:1.00
 F41 B:N971001 0.0 64.6 1.0
C13 B:N971001 1.3 60.2 1.0
C14 B:N971001 2.4 51.9 1.0
C12 B:N971001 2.4 65.5 1.0
N11 B:N971001 2.8 72.4 1.0
N19 B:N971001 2.8 50.8 1.0
O21 B:N971001 2.9 59.7 1.0
C20 B:N971001 3.1 55.8 1.0
F7 B:N971001 3.5 82.1 1.0
C15 B:N971001 3.6 51.2 1.0
N B:ASP711 3.6 42.9 1.0
C17 B:N971001 3.6 61.0 1.0
CB B:SER710 3.9 46.7 1.0
CA B:ASP711 3.9 43.2 1.0
OG B:SER710 4.0 47.8 1.0
C16 B:N971001 4.1 55.8 1.0
CB B:ASP711 4.2 48.8 1.0
C22 B:N971001 4.3 52.8 1.0
NZ B:LYS599 4.4 73.6 1.0
S8 B:N971001 4.4 82.8 1.0
CD1 B:ILE642 4.5 45.6 1.0
C5 B:N971001 4.6 84.4 1.0
C B:SER710 4.6 44.7 1.0
CA B:SER710 4.8 40.8 1.0
OD1 B:ASP711 4.8 65.4 1.0
CG B:ASP711 4.9 57.9 1.0
O9 B:N971001 4.9 88.6 1.0

Fluorine binding site 5 out of 6 in 6xdd

Go back to Fluorine Binding Sites List in 6xdd
Fluorine binding site 5 out of 6 in the Crystal Structure of IRE1 in Complex with G-3053


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of IRE1 in Complex with G-3053 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:87.3
occ:1.00
 F42 B:N971001 0.0 87.3 1.0
C2 B:N971001 1.3 83.1 1.0
C1 B:N971001 2.3 81.8 1.0
C3 B:N971001 2.4 81.2 1.0
CD1 B:TYR628 3.2 53.1 1.0
C6 B:N971001 3.6 83.4 1.0
C4 B:N971001 3.6 83.4 1.0
CG B:TYR628 3.7 51.6 1.0
CA B:VAL613 3.7 75.2 1.0
CG2 B:VAL613 3.8 67.6 1.0
CB B:TYR628 3.9 45.7 1.0
CB B:LEU616 3.9 77.7 1.0
CE1 B:TYR628 3.9 48.8 1.0
CG2 B:ILE640 4.0 52.3 1.0
C5 B:N971001 4.1 84.4 1.0
CB B:VAL613 4.2 70.0 1.0
N B:VAL613 4.4 78.5 1.0
O B:GLU612 4.4 81.9 1.0
CG1 B:VAL613 4.5 68.6 1.0
O B:VAL613 4.6 79.2 1.0
CG B:LEU616 4.6 80.1 1.0
C B:GLU612 4.7 81.7 1.0
C B:VAL613 4.7 77.1 1.0
CD2 B:TYR628 4.7 51.7 1.0
CD2 B:LEU616 4.7 79.8 1.0
CD1 B:LEU616 4.7 81.5 1.0
CG2 B:ILE642 4.8 46.1 1.0
CZ B:TYR628 4.9 49.0 1.0

Fluorine binding site 6 out of 6 in 6xdd

Go back to Fluorine Binding Sites List in 6xdd
Fluorine binding site 6 out of 6 in the Crystal Structure of IRE1 in Complex with G-3053


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of IRE1 in Complex with G-3053 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:82.1
occ:1.00
 F7 B:N971001 0.0 82.1 1.0
C5 B:N971001 1.4 84.4 1.0
C4 B:N971001 2.3 83.4 1.0
C6 B:N971001 2.4 83.4 1.0
N11 B:N971001 2.6 72.4 1.0
S8 B:N971001 2.8 82.8 1.0
C12 B:N971001 2.9 65.5 1.0
O9 B:N971001 3.0 88.6 1.0
N B:ASP711 3.4 42.9 1.0
C13 B:N971001 3.4 60.2 1.0
F41 B:N971001 3.5 64.6 1.0
C3 B:N971001 3.6 81.2 1.0
C1 B:N971001 3.6 81.8 1.0
C17 B:N971001 3.7 61.0 1.0
CG2 B:ILE626 3.7 49.1 1.0
CD2 B:PHE712 3.8 57.5 1.0
CE2 B:PHE712 4.0 59.8 1.0
CB B:SER710 4.1 46.7 1.0
CA B:SER710 4.1 40.8 1.0
C2 B:N971001 4.1 83.1 1.0
O10 B:N971001 4.1 87.0 1.0
CA B:ASP711 4.2 43.2 1.0
C B:SER710 4.2 44.7 1.0
C14 B:N971001 4.4 51.9 1.0
CD1 B:ILE642 4.4 45.6 1.0
N B:PHE712 4.5 42.1 1.0
C16 B:N971001 4.6 55.8 1.0
CD2 B:LEU616 4.6 79.8 1.0
C B:ASP711 4.9 44.9 1.0
C15 B:N971001 4.9 51.2 1.0
CG B:PHE712 5.0 52.0 1.0
CB B:ILE626 5.0 53.1 1.0

Reference:

R.E.Beveridge, H.A.Wallweber, A.Ashkenazi, M.Beresini, K.R.Clark, P.Gibbons, E.Ghiro, S.Kaufman, A.Larivee, M.Leblanc, J.P.Leclerc, A.Lemire, C.Ly, J.Rudolph, J.B.Schwarz, S.Srivastava, W.Wang, L.Zhao, M.G.Braun. Identification of Braf-Sparing Amino-Thienopyrimidines with Potent IRE1 Alpha Inhibitory Activity. Acs Med.Chem.Lett. V. 11 2389 2020.
ISSN: ISSN 1948-5875
PubMed: 33335661
DOI: 10.1021/ACSMEDCHEMLETT.0C00344
Page generated: Tue Jul 15 17:22:12 2025

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