Fluorine in PDB 6adg: Crystal Structures of IDH1 R132H in Complex with Ag-881

All present enzymatic activity of Crystal Structures of IDH1 R132H in Complex with Ag-881:
1.1.1.42;

The structure of Crystal Structures of IDH1 R132H in Complex with Ag-881, PDB code: 6adg was solved by R.Ma, C.H.Yun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.02 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	87.965, 197.253, 85.828, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 24.4

The structure of Crystal Structures of IDH1 R132H in Complex with Ag-881 also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structures of IDH1 R132H in Complex with Ag-881 (pdb code 6adg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 18 binding sites of Fluorine where determined in the Crystal Structures of IDH1 R132H in Complex with Ag-881, PDB code: 6adg:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 18 in the Crystal Structures of IDH1 R132H in Complex with Ag-881


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structures of IDH1 R132H in Complex with Ag-881 within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:47.0 occ:0.65 F04 A:9UO504 0.0 47.0 0.7 F04 A:9UO504 0.2 46.9 0.3 C03 A:9UO504 1.3 43.5 0.3 C03 A:9UO504 1.4 43.7 0.7 F06 A:9UO504 2.2 44.3 0.3 F05 A:9UO504 2.2 43.2 0.7 F06 A:9UO504 2.2 40.9 0.7 C02 A:9UO504 2.2 41.5 0.3 F05 A:9UO504 2.3 42.8 0.3 C02 A:9UO504 2.4 40.5 0.7 SD A:MET259 2.7 45.7 1.0 CG A:MET259 3.0 42.4 1.0 N07 A:9UO504 3.1 40.2 0.3 N07 A:9UO504 3.2 39.9 0.7 C01 A:9UO504 3.4 41.9 0.3 C01 A:9UO504 3.6 41.7 0.7 N27 A:9UO504 3.7 42.1 0.3 CE A:MET259 3.7 43.6 1.0 N27 A:9UO504 3.7 43.1 0.7 O A:VAL255 3.7 37.8 1.0 C08 A:9UO504 3.8 40.6 0.3 C08 A:9UO504 3.9 41.3 0.7 CB A:MET259 3.9 39.5 1.0 N A:MET259 4.3 37.5 1.0 CA A:MET259 4.3 37.8 1.0 CZ2 A:TRP124 4.5 37.0 1.0 C A:VAL255 4.6 39.2 1.0 C21 A:9UO504 4.8 41.7 0.3 CH2 A:TRP124 4.8 37.1 1.0 C19 A:9UO504 4.8 41.7 0.3 CB A:VAL255 4.8 39.7 1.0 C21 A:9UO504 4.8 44.0 0.7 C19 A:9UO504 4.9 41.7 0.7 CA A:VAL255 4.9 38.8 1.0 CB A:ALA258 4.9 33.5 1.0 N09 A:9UO504 5.0 40.6 0.3

Fluorine binding site 2 out of 18 in the Crystal Structures of IDH1 R132H in Complex with Ag-881


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structures of IDH1 R132H in Complex with Ag-881 within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:46.9 occ:0.35 F04 A:9UO504 0.0 46.9 0.3 F04 A:9UO504 0.2 47.0 0.7 C03 A:9UO504 1.4 43.5 0.3 C03 A:9UO504 1.4 43.7 0.7 F05 A:9UO504 2.2 43.2 0.7 F05 A:9UO504 2.2 42.8 0.3 F06 A:9UO504 2.2 44.3 0.3 F06 A:9UO504 2.3 40.9 0.7 C02 A:9UO504 2.4 41.5 0.3 C02 A:9UO504 2.5 40.5 0.7 SD A:MET259 2.7 45.7 1.0 CG A:MET259 2.9 42.4 1.0 N07 A:9UO504 3.3 40.2 0.3 N07 A:9UO504 3.4 39.9 0.7 C01 A:9UO504 3.5 41.9 0.3 CE A:MET259 3.6 43.6 1.0 C01 A:9UO504 3.6 41.7 0.7 O A:VAL255 3.7 37.8 1.0 CB A:MET259 3.8 39.5 1.0 N27 A:9UO504 3.8 42.1 0.3 N27 A:9UO504 3.9 43.1 0.7 C08 A:9UO504 4.0 40.6 0.3 C08 A:9UO504 4.1 41.3 0.7 N A:MET259 4.2 37.5 1.0 CA A:MET259 4.2 37.8 1.0 CZ2 A:TRP124 4.4 37.0 1.0 C A:VAL255 4.6 39.2 1.0 CH2 A:TRP124 4.7 37.1 1.0 C21 A:9UO504 4.9 41.7 0.3 CB A:ALA258 4.9 33.5 1.0 C A:ALA258 4.9 38.3 1.0 C21 A:9UO504 4.9 44.0 0.7 CB A:VAL255 4.9 39.7 1.0 CA A:VAL255 5.0 38.8 1.0 C19 A:9UO504 5.0 41.7 0.3

Fluorine binding site 3 out of 18 in the Crystal Structures of IDH1 R132H in Complex with Ag-881


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structures of IDH1 R132H in Complex with Ag-881 within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:43.2 occ:0.65 F05 A:9UO504 0.0 43.2 0.7 F05 A:9UO504 0.2 42.8 0.3 C03 A:9UO504 1.2 43.5 0.3 C03 A:9UO504 1.4 43.7 0.7 C02 A:9UO504 2.1 41.5 0.3 F06 A:9UO504 2.1 44.3 0.3 F04 A:9UO504 2.2 46.9 0.3 F06 A:9UO504 2.2 40.9 0.7 F04 A:9UO504 2.2 47.0 0.7 C01 A:9UO504 2.3 41.9 0.3 C02 A:9UO504 2.4 40.5 0.7 C01 A:9UO504 2.5 41.7 0.7 CH2 A:TRP124 2.9 37.1 1.0 CZ2 A:TRP124 3.0 37.0 1.0 N07 A:9UO504 3.2 40.2 0.3 N07 A:9UO504 3.5 39.9 0.7 CZ3 A:TRP124 4.2 35.9 1.0 CE2 A:TRP124 4.3 35.9 1.0 C08 A:9UO504 4.5 40.6 0.3 CB A:ALA258 4.5 33.5 1.0 CG2 A:VAL281 4.6 37.5 1.0 CG A:MET259 4.6 42.4 1.0 C08 A:9UO504 4.7 41.3 0.7 N A:MET259 4.8 37.5 1.0 SD A:MET259 4.8 45.7 1.0 N27 A:9UO504 4.8 42.1 0.3 CA A:MET259 5.0 37.8 1.0 C A:ALA258 5.0 38.3 1.0

Fluorine binding site 4 out of 18 in the Crystal Structures of IDH1 R132H in Complex with Ag-881


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structures of IDH1 R132H in Complex with Ag-881 within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:42.8 occ:0.35 F05 A:9UO504 0.0 42.8 0.3 F05 A:9UO504 0.2 43.2 0.7 C03 A:9UO504 1.4 43.5 0.3 C03 A:9UO504 1.5 43.7 0.7 F06 A:9UO504 2.2 44.3 0.3 F04 A:9UO504 2.2 46.9 0.3 F04 A:9UO504 2.3 47.0 0.7 F06 A:9UO504 2.3 40.9 0.7 C02 A:9UO504 2.4 41.5 0.3 C01 A:9UO504 2.5 41.9 0.3 C02 A:9UO504 2.6 40.5 0.7 CZ2 A:TRP124 2.8 37.0 1.0 C01 A:9UO504 2.8 41.7 0.7 CH2 A:TRP124 2.8 37.1 1.0 N07 A:9UO504 3.4 40.2 0.3 N07 A:9UO504 3.7 39.9 0.7 CE2 A:TRP124 4.1 35.9 1.0 CZ3 A:TRP124 4.1 35.9 1.0 CB A:ALA258 4.4 33.5 1.0 CG A:MET259 4.6 42.4 1.0 N A:MET259 4.6 37.5 1.0 CG2 A:VAL281 4.6 37.5 1.0 C08 A:9UO504 4.7 40.6 0.3 C A:ALA258 4.8 38.3 1.0 CA A:MET259 4.8 37.8 1.0 SD A:MET259 4.8 45.7 1.0 C08 A:9UO504 5.0 41.3 0.7 NE1 A:TRP124 5.0 33.9 1.0 O A:ALA258 5.0 38.3 1.0 O A:VAL255 5.0 37.8 1.0

Fluorine binding site 5 out of 18 in the Crystal Structures of IDH1 R132H in Complex with Ag-881


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structures of IDH1 R132H in Complex with Ag-881 within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:40.9 occ:0.65 F06 A:9UO504 0.0 40.9 0.7 F06 A:9UO504 0.1 44.3 0.3 C03 A:9UO504 1.4 43.7 0.7 C03 A:9UO504 1.4 43.5 0.3 F05 A:9UO504 2.2 43.2 0.7 F04 A:9UO504 2.2 47.0 0.7 F05 A:9UO504 2.3 42.8 0.3 F04 A:9UO504 2.3 46.9 0.3 C02 A:9UO504 2.4 40.5 0.7 C02 A:9UO504 2.4 41.5 0.3 N07 A:9UO504 2.4 40.2 0.3 N07 A:9UO504 2.5 39.9 0.7 C01 A:9UO504 3.2 41.7 0.7 C01 A:9UO504 3.3 41.9 0.3 C08 A:9UO504 3.4 40.6 0.3 O A:VAL255 3.6 37.8 1.0 C08 A:9UO504 3.7 41.3 0.7 CB A:ALA258 3.7 33.5 1.0 CA A:VAL255 3.8 38.8 1.0 CZ3 A:TRP267 3.9 35.7 1.0 CB A:VAL255 3.9 39.7 1.0 N27 A:9UO504 4.1 42.1 0.3 CH2 A:TRP267 4.1 31.2 1.0 C A:VAL255 4.2 39.2 1.0 N09 A:9UO504 4.2 40.6 0.3 N27 A:9UO504 4.2 43.1 0.7 CG A:MET259 4.3 42.4 1.0 OE1 A:GLN277 4.3 40.8 1.0 N09 A:9UO504 4.6 40.7 0.7 SD A:MET259 4.6 45.7 1.0 CG1 A:VAL255 4.6 32.0 1.0 N A:MET259 4.7 37.5 1.0 CZ2 A:TRP124 4.8 37.0 1.0 CA A:ALA258 4.9 32.5 1.0 CD A:GLN277 4.9 36.3 1.0 C A:ALA258 4.9 38.3 1.0 NE2 A:GLN277 4.9 34.6 1.0 CH2 A:TRP124 5.0 37.1 1.0

Fluorine binding site 6 out of 18 in the Crystal Structures of IDH1 R132H in Complex with Ag-881


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structures of IDH1 R132H in Complex with Ag-881 within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:44.3 occ:0.35 F06 A:9UO504 0.0 44.3 0.3 F06 A:9UO504 0.1 40.9 0.7 C03 A:9UO504 1.3 43.7 0.7 C03 A:9UO504 1.4 43.5 0.3 F05 A:9UO504 2.1 43.2 0.7 F04 A:9UO504 2.2 47.0 0.7 F05 A:9UO504 2.2 42.8 0.3 F04 A:9UO504 2.2 46.9 0.3 C02 A:9UO504 2.4 41.5 0.3 C02 A:9UO504 2.4 40.5 0.7 N07 A:9UO504 2.4 40.2 0.3 N07 A:9UO504 2.6 39.9 0.7 C01 A:9UO504 3.2 41.7 0.7 C01 A:9UO504 3.3 41.9 0.3 C08 A:9UO504 3.5 40.6 0.3 O A:VAL255 3.6 37.8 1.0 CB A:ALA258 3.7 33.5 1.0 C08 A:9UO504 3.7 41.3 0.7 CA A:VAL255 3.9 38.8 1.0 CZ3 A:TRP267 3.9 35.7 1.0 CB A:VAL255 4.0 39.7 1.0 N27 A:9UO504 4.1 42.1 0.3 C A:VAL255 4.2 39.2 1.0 CH2 A:TRP267 4.2 31.2 1.0 CG A:MET259 4.2 42.4 1.0 N27 A:9UO504 4.3 43.1 0.7 N09 A:9UO504 4.3 40.6 0.3 OE1 A:GLN277 4.4 40.8 1.0 SD A:MET259 4.5 45.7 1.0 N A:MET259 4.6 37.5 1.0 N09 A:9UO504 4.7 40.7 0.7 CZ2 A:TRP124 4.7 37.0 1.0 CG1 A:VAL255 4.7 32.0 1.0 CA A:ALA258 4.8 32.5 1.0 C A:ALA258 4.9 38.3 1.0 CH2 A:TRP124 4.9 37.1 1.0 CD A:GLN277 5.0 36.3 1.0

Fluorine binding site 7 out of 18 in the Crystal Structures of IDH1 R132H in Complex with Ag-881


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structures of IDH1 R132H in Complex with Ag-881 within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:68.4 occ:0.65 F24 A:9UO504 0.0 68.4 0.7 F24 A:9UO504 0.1 61.0 0.3 C23 A:9UO504 1.4 47.0 0.7 C23 A:9UO504 1.4 47.0 0.3 F25 A:9UO504 2.2 44.8 0.3 F26 A:9UO504 2.2 47.6 0.7 F25 A:9UO504 2.2 44.4 0.7 F26 A:9UO504 2.2 52.4 0.3 C21 A:9UO504 2.4 44.0 0.7 C21 A:9UO504 2.4 41.7 0.3 CG B:MET259 2.6 40.9 1.0 N20 A:9UO504 3.1 41.9 0.7 O B:VAL255 3.1 38.7 1.0 N20 A:9UO504 3.2 42.0 0.3 SD B:MET259 3.4 41.6 1.0 C22 A:9UO504 3.6 41.5 0.7 C22 A:9UO504 3.7 41.5 0.3 C19 A:9UO504 3.7 41.7 0.7 N27 A:9UO504 3.8 43.1 0.7 C19 A:9UO504 3.9 41.7 0.3 N27 A:9UO504 3.9 42.1 0.3 C B:VAL255 3.9 37.6 1.0 CB B:MET259 4.0 43.0 1.0 CB B:VAL255 4.0 38.3 1.0 CA B:VAL255 4.1 36.2 1.0 N B:MET259 4.2 36.3 1.0 CA B:MET259 4.4 37.1 1.0 OG A:SER280 4.6 56.3 1.0 CB B:ALA258 4.7 30.5 1.0 CG2 B:VAL255 4.7 39.4 1.0 N18 A:9UO504 4.7 41.5 0.7 CE B:MET259 4.8 39.3 1.0 C08 A:9UO504 4.9 41.3 0.7 CZ2 B:TRP124 4.9 42.0 1.0 C B:ALA258 5.0 35.0 1.0 N18 A:9UO504 5.0 41.5 0.3

Fluorine binding site 8 out of 18 in the Crystal Structures of IDH1 R132H in Complex with Ag-881


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structures of IDH1 R132H in Complex with Ag-881 within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:61.0 occ:0.35 F24 A:9UO504 0.0 61.0 0.3 F24 A:9UO504 0.1 68.4 0.7 C23 A:9UO504 1.3 47.0 0.7 C23 A:9UO504 1.4 47.0 0.3 F26 A:9UO504 2.2 47.6 0.7 F26 A:9UO504 2.2 52.4 0.3 F25 A:9UO504 2.2 44.8 0.3 F25 A:9UO504 2.3 44.4 0.7 C21 A:9UO504 2.3 44.0 0.7 C21 A:9UO504 2.4 41.7 0.3 CG B:MET259 2.7 40.9 1.0 N20 A:9UO504 3.0 41.9 0.7 N20 A:9UO504 3.1 42.0 0.3 O B:VAL255 3.2 38.7 1.0 SD B:MET259 3.4 41.6 1.0 C22 A:9UO504 3.5 41.5 0.7 C19 A:9UO504 3.6 41.7 0.7 C22 A:9UO504 3.6 41.5 0.3 N27 A:9UO504 3.7 43.1 0.7 C19 A:9UO504 3.8 41.7 0.3 N27 A:9UO504 3.8 42.1 0.3 C B:VAL255 4.0 37.6 1.0 CB B:VAL255 4.0 38.3 1.0 CB B:MET259 4.1 43.0 1.0 CA B:VAL255 4.1 36.2 1.0 N B:MET259 4.3 36.3 1.0 CA B:MET259 4.5 37.1 1.0 OG A:SER280 4.6 56.3 1.0 N18 A:9UO504 4.6 41.5 0.7 CG2 B:VAL255 4.6 39.4 1.0 CB B:ALA258 4.7 30.5 1.0 C08 A:9UO504 4.8 41.3 0.7 CE B:MET259 4.8 39.3 1.0 N18 A:9UO504 4.9 41.5 0.3 C08 A:9UO504 4.9 40.6 0.3

Fluorine binding site 9 out of 18 in the Crystal Structures of IDH1 R132H in Complex with Ag-881


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structures of IDH1 R132H in Complex with Ag-881 within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:44.4 occ:0.65 F25 A:9UO504 0.0 44.4 0.7 F25 A:9UO504 0.3 44.8 0.3 C23 A:9UO504 1.4 47.0 0.7 C23 A:9UO504 1.5 47.0 0.3 F26 A:9UO504 2.2 47.6 0.7 F24 A:9UO504 2.2 68.4 0.7 F24 A:9UO504 2.3 61.0 0.3 F26 A:9UO504 2.3 52.4 0.3 C21 A:9UO504 2.4 44.0 0.7 C22 A:9UO504 2.6 41.5 0.7 C21 A:9UO504 2.7 41.7 0.3 C22 A:9UO504 2.9 41.5 0.3 CZ2 B:TRP124 3.0 42.0 1.0 CH2 B:TRP124 3.2 36.8 1.0 N20 A:9UO504 3.5 41.9 0.7 CG B:MET259 3.7 40.9 1.0 N20 A:9UO504 3.8 42.0 0.3 CE2 B:TRP124 4.3 44.9 1.0 N B:MET259 4.4 36.3 1.0 CB B:ALA258 4.5 30.5 1.0 CA B:MET259 4.5 37.1 1.0 CZ3 B:TRP124 4.6 37.0 1.0 CB B:MET259 4.7 43.0 1.0 O B:VAL255 4.7 38.7 1.0 C19 A:9UO504 4.7 41.7 0.7 C B:ALA258 4.8 35.0 1.0 SD B:MET259 4.9 41.6 1.0 CG2 B:VAL281 4.9 32.1 1.0 CG2 B:VAL121 5.0 43.5 1.0

Fluorine binding site 10 out of 18 in the Crystal Structures of IDH1 R132H in Complex with Ag-881


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structures of IDH1 R132H in Complex with Ag-881 within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:44.8 occ:0.35 F25 A:9UO504 0.0 44.8 0.3 F25 A:9UO504 0.3 44.4 0.7 C23 A:9UO504 1.2 47.0 0.7 C23 A:9UO504 1.4 47.0 0.3 C21 A:9UO504 2.0 44.0 0.7 F26 A:9UO504 2.2 47.6 0.7 F24 A:9UO504 2.2 68.4 0.7 F26 A:9UO504 2.2 52.4 0.3 F24 A:9UO504 2.2 61.0 0.3 C22 A:9UO504 2.2 41.5 0.7 C21 A:9UO504 2.4 41.7 0.3 C22 A:9UO504 2.6 41.5 0.3 CZ2 B:TRP124 3.2 42.0 1.0 N20 A:9UO504 3.2 41.9 0.7 CH2 B:TRP124 3.3 36.8 1.0 N20 A:9UO504 3.6 42.0 0.3 CG B:MET259 3.9 40.9 1.0 C19 A:9UO504 4.4 41.7 0.7 CE2 B:TRP124 4.5 44.9 1.0 CZ3 B:TRP124 4.6 37.0 1.0 N B:MET259 4.7 36.3 1.0 C19 A:9UO504 4.8 41.7 0.3 CB B:ALA258 4.8 30.5 1.0 N27 A:9UO504 4.8 43.1 0.7 CG2 B:VAL281 4.8 32.1 1.0 CA B:MET259 4.8 37.1 1.0 O B:VAL255 4.9 38.7 1.0 CB B:MET259 4.9 43.0 1.0 SD B:MET259 5.0 41.6 1.0 N27 A:9UO504 5.0 42.1 0.3

R.Ma, C.H.Yun. Crystal Structures of Pan-Idh Inhibitor Ag-881 in Complex with Mutant Human IDH1 and IDH2 Biochem. Biophys. Res. V. 503 2912 2018COMMUN..
ISSN: ESSN 1090-2104
PubMed: 30131249
DOI: 10.1016/J.BBRC.2018.08.068