Fluorine in PDB 5trf: MDM2 in Complex with SAR405838

Protein crystallography data

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

Other elements in 5trf:

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

Chlorine (Cl) 10 atoms

Fluorine Binding Sites:

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 5trf

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

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

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

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

Go back to Fluorine Binding Sites List in 5trf
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

Reference:

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
Page generated: Sun Dec 13 12:38:28 2020

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