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

Protein crystallography data

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

Fluorine Binding Sites:

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 5m4h

Go back to Fluorine Binding Sites List in 5m4h
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 5m4h

Go back to Fluorine Binding Sites List in 5m4h
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 5m4h

Go back to Fluorine Binding Sites List in 5m4h
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

Reference:

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
Page generated: Tue Jul 15 05:10:40 2025

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