Fluorine in PDB 5oai: Structure of MDM2 with Low Molecular Weight Inhibitor

All present enzymatic activity of Structure of MDM2 with Low Molecular Weight Inhibitor:
2.3.2.27;

The structure of Structure of MDM2 with Low Molecular Weight Inhibitor, PDB code: 5oai was solved by A.Twarda-Clapa, C.G.Neochoritis, P.Grudnik, G.Dubin, A.Domling, T.A.Holak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.78 / 2.00
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	49.731, 59.216, 83.897, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 22.7

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

Chlorine

(Cl)

1 atom

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

Fluorine binding site 1 out of 3 in the Structure of MDM2 with Low Molecular Weight Inhibitor


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:39.9 occ:1.00 F A:B5K201 0.0 39.9 1.0 C14 A:B5K201 1.3 39.6 1.0 C13 A:B5K201 2.5 39.8 1.0 C15 A:B5K201 2.5 39.7 1.0 F2 A:B5K201 2.8 38.5 1.0 F1 A:B5K201 2.9 40.0 1.0 O A:HOH308 3.1 42.3 1.0 CD1 A:LEU54 3.3 32.2 1.0 CG A:LEU54 3.3 32.2 1.0 CE1 A:TYR100 3.3 35.2 1.0 C16 A:B5K201 3.7 40.9 1.0 C12 A:B5K201 3.7 40.4 1.0 ND1 A:HIS96 3.8 36.8 1.0 CD1 A:TYR100 4.0 34.8 1.0 CG A:HIS96 4.1 35.6 1.0 C11 A:B5K201 4.2 41.0 1.0 CB A:LEU54 4.2 31.8 1.0 CE1 A:HIS96 4.3 37.5 1.0 CD2 A:LEU54 4.3 31.6 1.0 CZ A:TYR100 4.4 34.6 1.0 CB A:HIS96 4.4 34.9 1.0 OH A:TYR100 4.5 34.6 1.0 CD2 A:HIS96 4.7 36.5 1.0 NE2 A:HIS96 4.8 37.9 1.0 CG1 A:ILE19 4.9 38.1 1.0

Fluorine binding site 2 out of 3 in the Structure of MDM2 with Low Molecular Weight Inhibitor


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:40.0 occ:1.00 F1 A:B5K201 0.0 40.0 1.0 C15 A:B5K201 1.3 39.7 1.0 C16 A:B5K201 2.4 40.9 1.0 C14 A:B5K201 2.5 39.6 1.0 F A:B5K201 2.9 39.9 1.0 O A:HOH308 3.6 42.3 1.0 C11 A:B5K201 3.7 41.0 1.0 C13 A:B5K201 3.8 39.8 1.0 CE1 A:HIS96 4.2 37.5 1.0 C12 A:B5K201 4.2 40.4 1.0 O A:HOH333 4.2 55.1 1.0 ND1 A:HIS96 4.4 36.8 1.0 O2 A:B5K201 4.5 41.7 1.0 O A:HOH315 4.5 62.8 1.0 C21 A:B5K201 4.6 41.2 1.0 C6 A:B5K201 4.7 40.1 1.0 CB A:LEU54 4.7 31.8 1.0 CG A:LEU54 4.7 32.2 1.0 C10 A:B5K201 4.9 42.0 1.0 F2 A:B5K201 4.9 38.5 1.0 NE2 A:HIS96 4.9 37.9 1.0 CD1 A:LEU54 4.9 32.2 1.0

Fluorine binding site 3 out of 3 in the Structure of MDM2 with Low Molecular Weight Inhibitor


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:38.5 occ:1.00 F2 A:B5K201 0.0 38.5 1.0 C13 A:B5K201 1.3 39.8 1.0 C12 A:B5K201 2.4 40.4 1.0 C14 A:B5K201 2.4 39.6 1.0 F A:B5K201 2.8 39.9 1.0 CD1 A:ILE99 3.2 27.2 1.0 CA A:HIS96 3.4 35.3 1.0 CB A:ILE99 3.4 27.4 1.0 CG2 A:ILE99 3.5 28.7 1.0 CG A:HIS96 3.5 35.6 1.0 CD2 A:HIS96 3.5 36.5 1.0 C11 A:B5K201 3.7 41.0 1.0 CB A:HIS96 3.7 34.9 1.0 C15 A:B5K201 3.8 39.7 1.0 CD1 A:LEU54 3.9 32.2 1.0 CG1 A:ILE99 3.9 27.0 1.0 O A:HIS96 4.0 30.0 1.0 ND1 A:HIS96 4.1 36.8 1.0 NE2 A:HIS96 4.2 37.9 1.0 C16 A:B5K201 4.2 40.9 1.0 C A:HIS96 4.2 32.2 1.0 N A:HIS96 4.4 39.5 1.0 CE1 A:HIS96 4.5 37.5 1.0 O A:GLU95 4.7 42.4 1.0 CD1 A:TYR100 4.7 34.8 1.0 O A:VAL93 4.8 34.9 1.0 CA A:ILE99 4.8 28.3 1.0 CG A:LEU54 4.8 32.2 1.0 C A:GLU95 4.8 44.6 1.0 CE1 A:TYR100 4.9 35.2 1.0 F1 A:B5K201 4.9 40.0 1.0 C10 A:B5K201 4.9 42.0 1.0

L.Skalniak, A.Twarda-Clapa, C.G.Neochoritis, E.Surmiak, M.Machula, A.Wisniewska, B.Labuzek, A.M.Ali, S.Krzanik, G.Dubin, M.Groves, A.Domling, T.A.Holak. A Fluorinated Indole-Based MDM2 Antagonist Selectively Inhibits the Growth of P53WTOSTEOSARCOMA Cells. Febs J. V. 286 1360 2019.
ISSN: ISSN 1742-464X
PubMed: 30715803
DOI: 10.1111/FEBS.14774