Fluorine in PDB 6e4w: Structure of Ampk Bound to Activator

All present enzymatic activity of Structure of Ampk Bound to Activator:
2.7.11.1; 2.7.11.26; 2.7.11.27; 2.7.11.31;

The structure of Structure of Ampk Bound to Activator, PDB code: 6e4w was solved by M.F.Calabrese, R.G.Kurumbail, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.58 / 3.35
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	123.970, 123.970, 402.120, 90.00, 90.00, 120.00
R / Rfree (%)	20.9 / 24.4

The structure of Structure of Ampk Bound to Activator also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Fluorine atom in the Structure of Ampk Bound to Activator (pdb code 6e4w). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Structure of Ampk Bound to Activator, PDB code: 6e4w:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Structure of Ampk Bound to Activator


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Ampk Bound to Activator within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:97.2 occ:1.00 F1 A:HUG602 0.0 97.2 1.0 C12 A:HUG602 1.3 96.7 1.0 C11 A:HUG602 2.3 0.9 1.0 C7 A:HUG602 2.4 90.2 1.0 O1 A:HUG602 2.4 0.0 1.0 C5 A:HUG602 2.8 80.2 1.0 C6 A:HUG602 2.8 83.3 1.0 C15 A:HUG602 3.0 0.1 1.0 C13 A:HUG602 3.0 0.0 1.0 C10 A:HUG602 3.6 99.6 1.0 C8 A:HUG602 3.6 90.2 1.0 NZ A:LYS29 3.7 0.5 1.0 C4 A:HUG602 4.0 76.7 1.0 CD A:LYS29 4.0 89.5 1.0 C1 A:HUG602 4.0 80.2 1.0 ND2 B:ASN111 4.1 0.9 1.0 C9 A:HUG602 4.2 94.1 1.0 CD B:ARG83 4.2 86.6 1.0 C14 A:HUG602 4.3 0.7 1.0 CD1 A:ILE46 4.4 72.3 1.0 O2 A:HUG602 4.4 0.2 1.0 CE A:LYS29 4.5 0.9 1.0 NE B:ARG83 4.5 95.6 1.0 CE A:LYS31 4.6 65.5 1.0 N1 A:HUG602 4.6 0.2 1.0 CG B:ASN111 4.7 0.1 1.0 F2 A:HUG602 4.7 89.4 1.0 CB B:ASN111 4.8 97.7 1.0 C3 A:HUG602 4.9 77.3 1.0 C2 A:HUG602 4.9 79.3 1.0

Fluorine binding site 2 out of 2 in the Structure of Ampk Bound to Activator


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Ampk Bound to Activator within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:89.4 occ:1.00 F2 A:HUG602 0.0 89.4 1.0 C8 A:HUG602 1.3 90.2 1.0 C9 A:HUG602 2.3 94.1 1.0 C7 A:HUG602 2.4 90.2 1.0 C1 A:HUG602 2.7 80.2 1.0 C6 A:HUG602 2.8 83.3 1.0 C10 A:HUG602 3.6 99.6 1.0 CZ A:PHE90 3.6 71.1 1.0 C12 A:HUG602 3.6 96.7 1.0 CE1 A:PHE90 3.8 70.1 1.0 C2 A:HUG602 3.9 79.3 1.0 CG1 B:VAL81 4.0 78.1 1.0 CD1 B:ILE115 4.0 84.9 1.0 C5 A:HUG602 4.0 80.2 1.0 CG2 B:VAL113 4.1 80.8 1.0 C11 A:HUG602 4.1 0.9 1.0 CD1 A:ILE46 4.3 72.3 1.0 CG2 B:VAL81 4.5 79.5 1.0 CG1 B:ILE115 4.5 80.3 1.0 CG2 A:ILE46 4.7 71.9 1.0 CD1 A:LEU18 4.7 76.3 1.0 CG1 B:VAL113 4.7 81.1 1.0 F1 A:HUG602 4.7 97.2 1.0 OD1 A:ASP88 4.8 93.5 1.0 CE2 A:PHE90 4.8 74.1 1.0 N1 A:HUG602 4.8 0.2 1.0 CB B:VAL81 4.9 79.2 1.0 C3 A:HUG602 4.9 77.3 1.0 CB B:VAL113 4.9 81.0 1.0 C4 A:HUG602 4.9 76.7 1.0 CG1 A:ILE46 5.0 68.9 1.0

T.F.Ryder, M.F.Calabrese, G.S.Walker, K.O.Cameron, A.R.Reyes, K.A.Borzilleri, J.Delmore, R.Miller, R.G.Kurumbail, J.Ward, D.W.Kung, J.A.Brown, D.J.Edmonds, H.Eng, A.C.Wolford, A.S.Kalgutkar. Acyl Glucuronide Metabolites of 6-Chloro-5-[4-(1-Hydroxycyclobutyl)Phenyl]-1 H-Indole-3-Carboxylic Acid (Pf-06409577) and Related Indole-3-Carboxylic Acid Derivatives Are Direct Activators of Adenosine Monophosphate-Activated Protein Kinase (Ampk). J. Med. Chem. V. 61 7273 2018.
ISSN: ISSN 1520-4804
PubMed: 30036059
DOI: 10.1021/ACS.JMEDCHEM.8B00807