Fluorine in PDB 5m4h: Application of Off-Rate Screening in the Identification of Novel Pan- Isoform Inhibitors of Pyruvate Dehydrogenase Kinase

The structure of Application of Off-Rate Screening in the Identification of Novel Pan- Isoform Inhibitors of Pyruvate Dehydrogenase Kinase, PDB code: 5m4h was solved by L.M.Baker, P.Brough, A.Surgenor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.57 / 2.00
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	64.011, 86.552, 96.957, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 31.7

The binding sites of Fluorine atom in the Application of Off-Rate Screening in the Identification of Novel Pan- Isoform Inhibitors of Pyruvate Dehydrogenase Kinase (pdb code 5m4h). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Application of Off-Rate Screening in the Identification of Novel Pan- Isoform Inhibitors of Pyruvate Dehydrogenase Kinase, PDB code: 5m4h:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Application of Off-Rate Screening in the Identification of Novel Pan- Isoform Inhibitors of Pyruvate Dehydrogenase Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Application of Off-Rate Screening in the Identification of Novel Pan- Isoform Inhibitors of Pyruvate Dehydrogenase Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:60.6 occ:1.00 F10 A:7FX301 0.0 60.6 1.0 C04 A:7FX301 1.3 56.1 1.0 F12 A:7FX301 2.2 63.9 1.0 F11 A:7FX301 2.2 55.5 1.0 C02 A:7FX301 2.3 45.9 1.0 C05 A:7FX301 2.8 39.8 1.0 N13 A:7FX301 2.9 45.6 1.0 C01 A:7FX301 3.0 34.4 1.0 CD A:LYS58 3.2 42.0 1.0 C03 A:7FX301 3.5 39.2 1.0 N09 A:7FX301 3.5 44.6 1.0 CG A:LYS58 3.6 35.9 1.0 N08 A:7FX301 3.7 33.2 1.0 CA A:ALA55 3.9 20.2 1.0 CG2 A:ILE96 3.9 19.4 1.0 CB A:LYS58 4.1 31.0 1.0 CB A:ALA55 4.2 19.2 1.0 N A:ALA55 4.2 19.3 1.0 O A:ASP54 4.2 18.3 1.0 NZ A:LYS58 4.3 49.6 1.0 CE A:LYS58 4.3 48.0 1.0 C06 A:7FX301 4.3 40.1 1.0 C07 A:7FX301 4.4 44.3 1.0 C A:ASP54 4.4 18.0 1.0 O A:HOH450 4.6 36.4 1.0 O A:HOH645 4.7 31.5 1.0 O A:HOH443 4.8 19.0 1.0 C22 A:7FX301 4.9 26.0 1.0 O A:HOH482 5.0 31.8 1.0

Fluorine binding site 2 out of 3 in the Application of Off-Rate Screening in the Identification of Novel Pan- Isoform Inhibitors of Pyruvate Dehydrogenase Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Application of Off-Rate Screening in the Identification of Novel Pan- Isoform Inhibitors of Pyruvate Dehydrogenase Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:55.5 occ:1.00 F11 A:7FX301 0.0 55.5 1.0 C04 A:7FX301 1.3 56.1 1.0 F12 A:7FX301 2.2 63.9 1.0 F10 A:7FX301 2.2 60.6 1.0 C02 A:7FX301 2.3 45.9 1.0 N09 A:7FX301 2.7 44.6 1.0 N13 A:7FX301 2.7 45.6 1.0 O A:HOH425 3.2 40.3 1.0 O A:HOH645 3.6 31.5 1.0 C05 A:7FX301 3.7 39.8 1.0 O A:HOH450 3.8 36.4 1.0 C07 A:7FX301 3.9 44.3 1.0 C03 A:7FX301 3.9 39.2 1.0 O A:HOH581 4.0 35.5 1.0 O A:GLY108 4.1 33.1 1.0 NZ A:LYS58 4.4 49.6 1.0 C01 A:7FX301 4.4 34.4 1.0 C06 A:7FX301 4.4 40.1 1.0 CD A:LYS58 4.5 42.0 1.0 O A:HOH595 4.5 39.3 1.0 N08 A:7FX301 4.7 33.2 1.0 CG A:LYS58 4.8 35.9 1.0 O A:HOH443 4.9 19.0 1.0 CB A:ASP54 4.9 16.8 1.0

Fluorine binding site 3 out of 3 in the Application of Off-Rate Screening in the Identification of Novel Pan- Isoform Inhibitors of Pyruvate Dehydrogenase Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Application of Off-Rate Screening in the Identification of Novel Pan- Isoform Inhibitors of Pyruvate Dehydrogenase Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:63.9 occ:1.00 F12 A:7FX301 0.0 63.9 1.0 C04 A:7FX301 1.3 56.1 1.0 F10 A:7FX301 2.2 60.6 1.0 F11 A:7FX301 2.2 55.5 1.0 C02 A:7FX301 2.3 45.9 1.0 O A:HOH450 2.5 36.4 1.0 C05 A:7FX301 2.8 39.8 1.0 NZ A:LYS58 3.2 49.6 1.0 O A:HOH608 3.4 49.5 1.0 CD A:LYS58 3.5 42.0 1.0 N13 A:7FX301 3.6 45.6 1.0 CE A:LYS58 3.8 48.0 1.0 O A:HOH595 3.9 39.3 1.0 C01 A:7FX301 3.9 34.4 1.0 O A:GLY108 4.0 33.1 1.0 N09 A:7FX301 4.2 44.6 1.0 CG A:LYS58 4.4 35.9 1.0 O A:HOH482 4.5 31.8 1.0 O A:HOH581 4.6 35.5 1.0 C03 A:7FX301 4.6 39.2 1.0 N08 A:7FX301 4.8 33.2 1.0 C A:GLY108 4.9 26.5 1.0 O A:HOH425 4.9 40.3 1.0 CA A:GLY108 5.0 29.4 1.0

P.A.Brough, L.Baker, S.Bedford, K.Brown, S.Chavda, V.Chell, J.D'alessandro, N.G.Davies, B.Davis, L.Le Strat, A.T.Macias, D.Maddox, P.C.Mahon, A.J.Massey, N.Matassova, S.Mckenna, J.W.Meissner, J.D.Moore, J.B.Murray, C.J.Northfield, C.Parry, R.Parsons, S.D.Roughley, T.Shaw, H.Simmonite, S.Stokes, A.Surgenor, E.Stefaniak, A.Robertson, Y.Wang, P.Webb, N.Whitehead, M.Wood. Application of Off-Rate Screening in the Identification of Novel Pan-Isoform Inhibitors of Pyruvate Dehydrogenase Kinase. J. Med. Chem. V. 60 2271 2017.
ISSN: ISSN 1520-4804
PubMed: 28199108
DOI: 10.1021/ACS.JMEDCHEM.6B01478