Fluorine in PDB 5trf: MDM2 in Complex with SAR405838

The structure of MDM2 in Complex with SAR405838, PDB code: 5trf was solved by J.L.Meagher, J.A.Stuckey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.09 / 2.10
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	138.849, 138.849, 83.707, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 20.8

The structure of MDM2 in Complex with SAR405838 also contains other interesting chemical elements:

Chlorine

(Cl)

10 atoms

The binding sites of Fluorine atom in the MDM2 in Complex with SAR405838 (pdb code 5trf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the MDM2 in Complex with SAR405838, PDB code: 5trf:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in the MDM2 in Complex with SAR405838


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of MDM2 in Complex with SAR405838 within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:14.7 occ:1.00 F A:7HC201 0.0 14.7 1.0 C21 A:7HC201 1.3 14.5 1.0 C20 A:7HC201 2.3 13.3 1.0 C16 A:7HC201 2.4 15.8 1.0 CL1 A:7HC201 2.8 16.6 1.0 C15 A:7HC201 2.9 17.6 1.0 CD2 A:HIS96 3.1 17.1 1.0 C28 A:7HC201 3.2 14.2 1.0 C29 A:7HC201 3.2 14.0 1.0 CD1 A:ILE99 3.3 9.9 1.0 NE2 A:HIS96 3.3 16.7 1.0 C22 A:7HC201 3.5 15.9 1.0 O A:VAL93 3.6 20.0 1.0 C19 A:7HC201 3.6 12.8 1.0 C17 A:7HC201 3.7 16.7 1.0 C27 A:7HC201 3.8 15.6 1.0 CG A:HIS96 3.8 15.8 1.0 C24 A:7HC201 4.0 14.8 1.0 CE1 A:HIS96 4.1 17.0 1.0 C18 A:7HC201 4.1 15.6 1.0 CG2 A:ILE99 4.3 12.2 1.0 CD1 A:LEU54 4.4 12.3 1.0 C7 A:7HC201 4.4 19.4 1.0 ND1 A:HIS96 4.4 17.1 1.0 C26 A:7HC201 4.4 16.7 1.0 C23 A:7HC201 4.4 15.9 1.0 O1 A:7HC201 4.5 20.0 1.0 CG1 A:ILE99 4.5 11.3 1.0 CB A:ILE99 4.5 10.8 1.0 C25 A:7HC201 4.5 13.4 1.0 C A:VAL93 4.6 19.7 1.0 N3 A:7HC201 4.6 13.7 1.0 CB A:HIS96 4.6 12.9 1.0 CA A:HIS96 4.7 12.5 1.0 C8 A:7HC201 4.7 20.0 1.0 C6 A:7HC201 4.7 15.4 1.0

Fluorine binding site 2 out of 5 in the MDM2 in Complex with SAR405838


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of MDM2 in Complex with SAR405838 within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:17.8 occ:1.00 F B:7HC201 0.0 17.8 1.0 C21 B:7HC201 1.3 18.3 1.0 C20 B:7HC201 2.3 18.9 1.0 C16 B:7HC201 2.4 18.6 1.0 CL1 B:7HC201 2.8 19.0 1.0 C15 B:7HC201 2.9 20.7 1.0 C28 B:7HC201 3.1 18.6 1.0 CD2 B:HIS96 3.2 18.3 1.0 C29 B:7HC201 3.3 18.8 1.0 CD1 B:ILE99 3.4 12.4 1.0 NE2 B:HIS96 3.4 18.2 1.0 C22 B:7HC201 3.6 20.5 1.0 C19 B:7HC201 3.6 14.7 1.0 C17 B:7HC201 3.7 17.9 1.0 O B:VAL93 3.7 21.9 1.0 C27 B:7HC201 3.8 16.6 1.0 CG B:HIS96 4.0 16.6 1.0 C24 B:7HC201 4.0 16.9 1.0 C18 B:7HC201 4.1 17.8 1.0 CG2 B:ILE99 4.2 16.2 1.0 CE1 B:HIS96 4.2 17.6 1.0 CD1 B:LEU54 4.3 14.7 1.0 C7 B:7HC201 4.4 22.5 1.0 O1 B:7HC201 4.4 25.1 1.0 CB B:ILE99 4.5 14.9 1.0 C23 B:7HC201 4.5 21.0 1.0 C26 B:7HC201 4.5 19.0 1.0 CG1 B:ILE99 4.5 14.2 1.0 ND1 B:HIS96 4.6 17.0 1.0 C25 B:7HC201 4.6 15.1 1.0 N3 B:7HC201 4.7 16.7 1.0 C8 B:7HC201 4.7 24.1 1.0 CA B:HIS96 4.7 13.9 1.0 C6 B:7HC201 4.8 20.2 1.0 CB B:HIS96 4.8 13.8 1.0 C B:VAL93 4.8 21.8 1.0

Fluorine binding site 3 out of 5 in the MDM2 in Complex with SAR405838


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of MDM2 in Complex with SAR405838 within 5.0Å range: probe atom residue distance (Å) B Occ C:F201 b:16.7 occ:1.00 F C:7HC201 0.0 16.7 1.0 C21 C:7HC201 1.3 17.7 1.0 C20 C:7HC201 2.3 17.9 1.0 C16 C:7HC201 2.4 18.8 1.0 CL1 C:7HC201 2.8 18.1 1.0 C15 C:7HC201 2.9 19.2 1.0 CD2 C:HIS96 3.1 17.5 1.0 C28 C:7HC201 3.1 15.8 1.0 C29 C:7HC201 3.2 16.5 1.0 NE2 C:HIS96 3.4 17.5 1.0 CD1 C:ILE99 3.4 11.0 1.0 C22 C:7HC201 3.5 18.7 1.0 C19 C:7HC201 3.6 15.1 1.0 O C:VAL93 3.7 16.5 1.0 C17 C:7HC201 3.7 18.6 1.0 C27 C:7HC201 3.8 16.1 1.0 CG C:HIS96 3.9 16.5 1.0 C24 C:7HC201 4.0 17.7 1.0 C18 C:7HC201 4.1 17.6 1.0 CE1 C:HIS96 4.2 17.7 1.0 CG2 C:ILE99 4.3 13.6 1.0 C7 C:7HC201 4.3 22.2 1.0 O1 C:7HC201 4.3 23.3 1.0 CD1 C:LEU54 4.4 15.6 1.0 C26 C:7HC201 4.4 16.5 1.0 C23 C:7HC201 4.5 18.0 1.0 CB C:ILE99 4.5 13.0 1.0 C25 C:7HC201 4.6 15.4 1.0 ND1 C:HIS96 4.6 18.4 1.0 CG1 C:ILE99 4.6 13.2 1.0 N3 C:7HC201 4.7 17.3 1.0 C8 C:7HC201 4.7 23.5 1.0 CA C:HIS96 4.7 13.8 1.0 CB C:HIS96 4.7 13.7 1.0 C6 C:7HC201 4.7 19.4 1.0 C C:VAL93 4.8 18.1 1.0

Fluorine binding site 4 out of 5 in the MDM2 in Complex with SAR405838


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of MDM2 in Complex with SAR405838 within 5.0Å range: probe atom residue distance (Å) B Occ D:F201 b:17.1 occ:1.00 F D:7HC201 0.0 17.1 1.0 C21 D:7HC201 1.3 18.9 1.0 C20 D:7HC201 2.3 18.8 1.0 C16 D:7HC201 2.4 20.4 1.0 C15 D:7HC201 2.8 23.6 1.0 CL1 D:7HC201 2.9 20.2 1.0 CD2 D:HIS96 3.1 20.3 1.0 C28 D:7HC201 3.1 18.6 1.0 C29 D:7HC201 3.2 20.2 1.0 CD1 D:ILE99 3.2 14.9 1.0 NE2 D:HIS96 3.3 20.3 1.0 C22 D:7HC201 3.5 22.0 1.0 O D:VAL93 3.6 22.9 1.0 C19 D:7HC201 3.6 18.2 1.0 C17 D:7HC201 3.7 18.3 1.0 C27 D:7HC201 3.8 20.2 1.0 CG D:HIS96 3.8 19.0 1.0 C24 D:7HC201 4.0 20.4 1.0 C18 D:7HC201 4.1 19.4 1.0 CE1 D:HIS96 4.1 20.2 1.0 C7 D:7HC201 4.3 25.9 1.0 CG2 D:ILE99 4.3 15.5 1.0 CD1 D:LEU54 4.4 17.2 1.0 C26 D:7HC201 4.4 20.6 1.0 C23 D:7HC201 4.4 20.9 1.0 ND1 D:HIS96 4.5 20.3 1.0 CG1 D:ILE99 4.5 16.8 1.0 C D:VAL93 4.5 24.4 1.0 CB D:ILE99 4.5 16.4 1.0 C25 D:7HC201 4.5 18.1 1.0 N3 D:7HC201 4.6 19.9 1.0 O1 D:7HC201 4.6 30.6 1.0 CB D:HIS96 4.7 17.1 1.0 CA D:HIS96 4.7 17.1 1.0 C6 D:7HC201 4.7 25.1 1.0 C8 D:7HC201 4.8 30.0 1.0 CA D:VAL93 4.9 23.5 1.0

Fluorine binding site 5 out of 5 in the MDM2 in Complex with SAR405838


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of MDM2 in Complex with SAR405838 within 5.0Å range: probe atom residue distance (Å) B Occ E:F201 b:23.3 occ:1.00 F E:7HC201 0.0 23.3 1.0 C21 E:7HC201 1.3 25.0 1.0 C20 E:7HC201 2.3 26.9 1.0 C16 E:7HC201 2.4 27.1 1.0 C15 E:7HC201 2.8 26.2 1.0 CL1 E:7HC201 2.9 26.9 1.0 CD2 E:HIS96 3.1 28.2 1.0 C28 E:7HC201 3.2 25.5 1.0 NE2 E:HIS96 3.2 28.2 1.0 C29 E:7HC201 3.3 27.5 1.0 CD1 E:ILE99 3.4 23.3 1.0 O E:VAL93 3.5 30.1 1.0 C22 E:7HC201 3.6 28.6 1.0 C19 E:7HC201 3.6 23.8 1.0 C17 E:7HC201 3.7 26.0 1.0 CG E:HIS96 3.8 25.9 1.0 C27 E:7HC201 3.9 24.6 1.0 CE1 E:HIS96 4.0 28.0 1.0 C24 E:7HC201 4.1 28.1 1.0 C18 E:7HC201 4.1 25.6 1.0 O1 E:7HC201 4.3 26.7 1.0 CG2 E:ILE99 4.3 19.9 1.0 CD1 E:LEU54 4.3 19.9 1.0 C7 E:7HC201 4.3 29.5 1.0 ND1 E:HIS96 4.4 28.1 1.0 C23 E:7HC201 4.5 29.3 1.0 C26 E:7HC201 4.5 24.3 1.0 CG1 E:ILE99 4.5 21.0 1.0 CB E:ILE99 4.5 20.3 1.0 C E:VAL93 4.6 30.4 1.0 C8 E:7HC201 4.6 30.1 1.0 C25 E:7HC201 4.6 24.3 1.0 N3 E:7HC201 4.7 27.5 1.0 CB E:HIS96 4.7 21.9 1.0 CA E:HIS96 4.7 20.4 1.0 C6 E:7HC201 4.7 28.5 1.0

S.Wang, W.Sun, Y.Zhao, D.Mceachern, I.Meaux, C.Barriere, J.A.Stuckey, J.L.Meagher, L.Bai, L.Liu, C.G.Hoffman-Luca, J.Lu, S.Shangary, S.Yu, D.Bernard, A.Aguilar, O.Dos-Santos, L.Besret, S.Guerif, P.Pannier, D.Gorge-Bernat, L.Debussche. SAR405838: An Optimized Inhibitor of MDM2-P53 Interaction That Induces Complete and Durable Tumor Regression. Cancer Res. V. 74 5855 2014.
ISSN: ESSN 1538-7445
PubMed: 25145672
DOI: 10.1158/0008-5472.CAN-14-0799