Fluorine in PDB 6bkz: Novel Modes of Inhibition of Wild-Type IDH1: Non-Equivalent Allosteric Inhibition with CMPD3

All present enzymatic activity of Novel Modes of Inhibition of Wild-Type IDH1: Non-Equivalent Allosteric Inhibition with CMPD3:
1.1.1.42;

The structure of Novel Modes of Inhibition of Wild-Type IDH1: Non-Equivalent Allosteric Inhibition with CMPD3, PDB code: 6bkz was solved by C.G.Jakob, W.Qiu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.39 / 2.01
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	83.463, 83.463, 299.255, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 20.4

The binding sites of Fluorine atom in the Novel Modes of Inhibition of Wild-Type IDH1: Non-Equivalent Allosteric Inhibition with CMPD3 (pdb code 6bkz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Novel Modes of Inhibition of Wild-Type IDH1: Non-Equivalent Allosteric Inhibition with CMPD3, PDB code: 6bkz:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Novel Modes of Inhibition of Wild-Type IDH1: Non-Equivalent Allosteric Inhibition with CMPD3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Novel Modes of Inhibition of Wild-Type IDH1: Non-Equivalent Allosteric Inhibition with CMPD3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:48.7 occ:1.00 F A:DWM502 0.0 48.7 1.0 C13 A:DWM502 1.4 43.9 1.0 C14 A:DWM502 2.4 39.7 1.0 C12 A:DWM502 2.4 40.9 1.0 SD A:MET259 3.3 57.8 1.0 CG1 A:VAL255 3.3 39.1 1.0 CG A:MET259 3.5 50.8 1.0 C15 A:DWM502 3.6 37.8 1.0 C11 A:DWM502 3.6 38.0 1.0 O A:VAL255 3.7 40.9 1.0 C10 A:DWM502 4.1 35.4 1.0 CA A:VAL255 4.2 36.2 1.0 CB A:VAL255 4.2 39.3 1.0 C A:VAL255 4.3 41.7 1.0 CB A:ALA258 4.4 39.1 1.0 CG2 A:VAL255 4.6 39.2 1.0 N A:MET259 4.6 39.3 1.0 CB A:MET259 4.8 44.5 1.0 CZ2 A:TRP124 4.9 36.1 1.0 CA A:MET259 4.9 40.8 1.0 C4 B:DWM502 5.0 34.9 1.0 CE A:MET259 5.0 55.1 1.0

Fluorine binding site 2 out of 2 in the Novel Modes of Inhibition of Wild-Type IDH1: Non-Equivalent Allosteric Inhibition with CMPD3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Novel Modes of Inhibition of Wild-Type IDH1: Non-Equivalent Allosteric Inhibition with CMPD3 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:31.8 occ:1.00 F B:DWM502 0.0 31.8 1.0 C13 B:DWM502 1.4 29.4 1.0 C14 B:DWM502 2.3 30.3 1.0 C12 B:DWM502 2.4 25.2 1.0 O B:VAL255 3.5 28.3 1.0 CG1 B:VAL255 3.6 29.0 1.0 CB B:ALA258 3.6 28.6 1.0 C15 B:DWM502 3.6 29.7 1.0 C11 B:DWM502 3.6 27.0 1.0 CG B:MET259 3.8 30.2 1.0 CA B:VAL255 3.8 25.5 1.0 CZ3 B:TRP267 3.9 25.7 1.0 CH2 B:TRP267 3.9 25.8 1.0 C B:VAL255 4.1 29.3 1.0 C10 B:DWM502 4.1 29.1 1.0 CB B:VAL255 4.1 29.5 1.0 CG1 A:VAL276 4.3 31.9 1.0 SD B:MET259 4.5 34.1 1.0 CG2 B:VAL255 4.5 29.7 1.0 N B:MET259 4.5 24.8 1.0 CZ2 B:TRP124 4.7 28.6 1.0 CA B:ALA258 4.8 27.5 1.0 C B:ALA258 4.9 27.4 1.0 O B:MET254 4.9 29.1 1.0 CH2 B:TRP124 5.0 27.8 1.0 CB B:MET259 5.0 27.7 1.0

C.G.Jakob, A.K.Upadhyay, P.L.Donner, E.Nicholl, S.N.Addo, W.Qiu, C.Ling, S.M.Gopalakrishnan, M.Torrent, S.P.Cepa, J.Shanley, A.R.Shoemaker, C.C.Sun, A.Vasudevan, K.R.Woller, J.B.Shotwell, B.Shaw, Z.Bian, J.E.Hutti. Novel Modes of Inhibition of Wild-Type Isocitrate Dehydrogenase 1 (IDH1): Direct Covalent Modification of HIS315. J. Med. Chem. V. 61 6647 2018.
ISSN: ISSN 1520-4804
PubMed: 30004704
DOI: 10.1021/ACS.JMEDCHEM.8B00305