Fluorine in PDB 5j7f: Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker.

The structure of Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker., PDB code: 5j7f was solved by A.Twarda-Clapa, K.Kubica, K.Guzik, G.Dubin, T.A.Holak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	87.38 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.758, 174.750, 37.810, 90.00, 93.48, 90.00
R / Rfree (%)	18.3 / 24.2

The structure of Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker. also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Fluorine atom in the Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker. (pdb code 5j7f). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker., PDB code: 5j7f:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker. within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:35.7 occ:1.00 F A:6GG201 0.0 35.7 1.0 C40 A:6GG201 1.3 31.3 1.0 C41 A:6GG201 2.4 28.1 1.0 C39 A:6GG201 2.4 28.6 1.0 CD2 A:TYR67 3.1 32.4 1.0 CG2 A:ILE61 3.3 27.7 1.0 C42 A:6GG201 3.6 28.8 1.0 CA A:MET62 3.6 32.9 1.0 C38 A:6GG201 3.6 29.0 1.0 N A:MET62 3.7 31.3 1.0 CG A:TYR67 3.8 32.4 1.0 CE2 A:TYR67 3.8 35.6 1.0 C A:ILE61 3.8 29.8 1.0 SD A:MET62 3.9 42.8 1.0 CB A:TYR67 3.9 32.5 1.0 O A:ILE61 4.0 30.9 1.0 CB A:MET62 4.0 33.2 1.0 CB A:ILE61 4.0 27.8 1.0 C37 A:6GG201 4.1 27.9 1.0 C12 D:6GG201 4.3 43.5 1.0 CA A:ILE61 4.6 28.3 1.0 CG A:MET62 4.6 38.1 1.0 N A:TYR67 4.7 30.8 1.0 CE D:MET62 4.7 48.2 1.0 O A:GLY58 4.8 30.9 1.0 C3 D:6GG201 4.8 40.6 1.0 C A:MET62 4.9 34.2 1.0 CA A:TYR67 4.9 32.7 1.0 CD1 A:TYR67 5.0 34.0 1.0 CZ A:TYR67 5.0 36.5 1.0

Fluorine binding site 2 out of 4 in the Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker. within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:34.2 occ:1.00 F B:6GG201 0.0 34.2 1.0 C40 B:6GG201 1.3 28.7 1.0 C39 B:6GG201 2.3 28.4 1.0 C41 B:6GG201 2.3 30.0 1.0 CG2 B:ILE61 3.1 29.8 1.0 CD2 B:TYR67 3.1 31.9 1.0 C38 B:6GG201 3.5 29.6 1.0 C42 B:6GG201 3.6 25.3 1.0 CA B:MET62 3.6 31.2 1.0 N B:MET62 3.6 29.6 1.0 C B:ILE61 3.8 30.4 1.0 CE2 B:TYR67 3.8 32.3 1.0 CG B:TYR67 3.9 31.4 1.0 O B:ILE61 3.9 29.0 1.0 C37 B:6GG201 4.0 28.7 1.0 CB B:MET62 4.0 31.1 1.0 CB B:ILE61 4.0 29.3 1.0 CB B:TYR67 4.0 31.1 1.0 SD B:MET62 4.1 29.8 0.5 C13 C:6GG201 4.1 46.4 1.0 CA B:ILE61 4.6 29.5 1.0 O B:GLY58 4.6 34.9 1.0 CG B:MET62 4.9 31.0 0.5 C16 C:6GG201 4.9 44.0 1.0 N B:TYR67 4.9 30.8 1.0 C3 C:6GG201 4.9 38.1 1.0 C B:MET62 4.9 33.7 1.0

Fluorine binding site 3 out of 4 in the Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker. within 5.0Å range: probe atom residue distance (Å) B Occ C:F201 b:39.3 occ:1.00 F C:6GG201 0.0 39.3 1.0 C40 C:6GG201 1.3 31.7 1.0 C41 C:6GG201 2.3 29.6 1.0 C39 C:6GG201 2.4 28.8 1.0 CG2 C:ILE61 3.0 27.2 1.0 CD2 C:TYR67 3.1 30.6 1.0 CG C:MET62 3.5 32.3 0.5 C42 C:6GG201 3.6 31.4 1.0 C38 C:6GG201 3.6 27.6 1.0 N C:MET62 3.7 30.2 1.0 CA C:MET62 3.7 31.7 1.0 CG C:TYR67 3.8 32.2 1.0 C C:ILE61 3.8 29.4 1.0 CE2 C:TYR67 3.9 31.7 1.0 O C:ILE61 3.9 27.1 1.0 CB C:TYR67 4.0 31.9 1.0 CB C:ILE61 4.0 27.2 1.0 C37 C:6GG201 4.0 29.5 1.0 CB C:MET62 4.1 33.1 1.0 C16 B:6GG201 4.4 39.3 1.0 C12 B:6GG201 4.5 38.8 1.0 O C:GLY58 4.6 31.0 1.0 CA C:ILE61 4.6 27.4 1.0 N C:TYR67 4.8 30.6 1.0 C3 B:6GG201 4.9 33.3 1.0 CA C:TYR67 5.0 31.6 1.0 CD1 C:TYR67 5.0 32.0 1.0 SD C:MET62 5.0 30.4 0.5

Fluorine binding site 4 out of 4 in the Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker. within 5.0Å range: probe atom residue distance (Å) B Occ D:F201 b:35.9 occ:1.00 F D:6GG201 0.0 35.9 1.0 C40 D:6GG201 1.3 33.7 1.0 C39 D:6GG201 2.4 33.3 1.0 C41 D:6GG201 2.4 30.2 1.0 CD2 D:TYR67 3.1 31.2 1.0 CG2 D:ILE61 3.2 31.3 1.0 C38 D:6GG201 3.6 30.6 1.0 CG D:TYR67 3.6 31.9 1.0 C42 D:6GG201 3.6 31.9 1.0 CG D:MET62 3.7 40.6 1.0 N D:MET62 3.7 32.6 1.0 CB D:TYR67 3.7 31.8 1.0 CA D:MET62 3.8 34.2 1.0 C D:ILE61 3.9 31.5 1.0 CE2 D:TYR67 3.9 32.4 1.0 CB D:ILE61 4.0 30.6 1.0 O D:ILE61 4.0 31.0 1.0 C37 D:6GG201 4.1 30.3 1.0 CB D:MET62 4.3 37.4 1.0 C13 A:6GG201 4.5 29.8 1.0 O D:GLY58 4.6 35.4 1.0 C12 A:6GG201 4.6 30.6 1.0 CA D:ILE61 4.6 30.6 1.0 CD1 D:TYR67 4.7 31.8 1.0 N D:TYR67 4.7 32.6 1.0 CA D:TYR67 4.8 32.0 1.0 C16 A:6GG201 4.9 33.9 1.0 O D:GLN72 4.9 34.0 1.0 CZ D:TYR67 4.9 32.0 1.0 CE D:MET62 5.0 48.2 1.0

A.Twarda-Clapa, S.Krzanik, K.Kubica, K.Guzik, B.Labuzek, C.G.Neochoritis, K.Khoury, K.Kowalska, M.Czub, G.Dubin, A.Domling, L.Skalniak, T.A.Holak. 1,4,5-Trisubstituted Imidazole-Based P53-MDM2/Mdmx Antagonists with Aliphatic Linkers For Conjugation with Biological Carriers. J. Med. Chem. V. 60 4234 2017.
ISSN: ISSN 1520-4804
PubMed: 28482147
DOI: 10.1021/ACS.JMEDCHEM.7B00104