Fluorine in PDB 3vbg: Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443

The structure of Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443, PDB code: 3vbg was solved by C.M.Lukacs, C.A.Janson, B.J.Graves, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.80
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	64.392, 64.392, 167.587, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 22

The structure of Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443 also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Fluorine atom in the Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443 (pdb code 3vbg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443, PDB code: 3vbg:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in the Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:0.2 occ:1.00 F25 A:03M1 0.0 0.2 1.0 C23 A:03M1 1.3 0.3 1.0 C22 A:03M1 2.3 0.3 1.0 C24 A:03M1 2.3 0.8 1.0 F26 A:03M1 2.6 0.4 1.0 CG1 B:VAL93 2.9 74.4 1.0 C19 A:03M1 3.6 0.8 1.0 CD1 B:ILE99 3.6 0.2 1.0 C21 A:03M1 3.7 0.7 1.0 CB B:VAL93 3.7 85.3 1.0 CE1 B:PHE91 3.8 98.6 1.0 CZ B:PHE91 4.1 84.0 1.0 C20 A:03M1 4.2 0.1 1.0 CA B:VAL93 4.2 91.6 1.0 CG2 B:ILE99 4.4 94.6 1.0 CG1 B:ILE99 4.6 0.8 1.0 O B:HOH6 4.6 0.4 1.0 C18 A:03M1 4.7 0.9 1.0 CL B:03M1 4.8 0.0 1.0

Fluorine binding site 2 out of 8 in the Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:0.4 occ:1.00 F26 A:03M1 0.0 0.4 1.0 C22 A:03M1 1.3 0.3 1.0 C23 A:03M1 2.2 0.3 1.0 C21 A:03M1 2.4 0.7 1.0 F25 A:03M1 2.6 0.2 1.0 C24 A:03M1 3.5 0.8 1.0 C20 A:03M1 3.6 0.1 1.0 CB B:LEU57 3.6 89.5 1.0 CD1 B:LEU57 4.0 75.7 1.0 C19 A:03M1 4.0 0.8 1.0 CD1 B:ILE61 4.1 82.1 1.0 CZ B:PHE91 4.3 84.0 1.0 CG B:LEU57 4.4 91.5 1.0 CL B:03M1 4.7 0.0 1.0 N B:GLY58 4.7 87.3 1.0 CD2 B:LEU54 4.8 65.2 1.0 CE1 B:PHE91 4.8 98.6 1.0 C B:LEU57 4.8 87.9 1.0 CA B:LEU57 4.8 88.5 1.0 CG1 B:ILE61 4.9 76.7 1.0 CG2 B:ILE99 4.9 94.6 1.0

Fluorine binding site 3 out of 8 in the Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1 b:0.8 occ:1.00 F25 B:03M1 0.0 0.8 1.0 C23 B:03M1 1.4 0.9 1.0 C22 B:03M1 2.3 0.1 1.0 C24 B:03M1 2.4 0.5 1.0 F26 B:03M1 2.6 1.0 1.0 CD1 A:ILE99 3.2 82.2 1.0 CG2 A:ILE99 3.4 80.5 1.0 C19 B:03M1 3.7 0.7 1.0 C21 B:03M1 3.7 0.2 1.0 CG1 A:VAL93 3.7 74.5 1.0 CB A:VAL93 4.0 89.0 1.0 CE1 A:PHE91 4.2 70.1 1.0 C20 B:03M1 4.2 0.8 1.0 CG1 A:ILE99 4.3 81.1 1.0 CA A:VAL93 4.3 90.5 1.0 CB A:ILE99 4.4 96.3 1.0 C18 B:03M1 4.9 0.9 1.0 O A:VAL93 5.0 0.4 1.0 CZ A:PHE91 5.0 75.2 1.0

Fluorine binding site 4 out of 8 in the Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1 b:1.0 occ:1.00 F26 B:03M1 0.0 1.0 1.0 C22 B:03M1 1.3 0.1 1.0 C23 B:03M1 2.3 0.9 1.0 C21 B:03M1 2.4 0.2 1.0 F25 B:03M1 2.6 0.8 1.0 CB A:LEU57 3.3 90.0 1.0 CD1 A:LEU57 3.4 83.8 1.0 C24 B:03M1 3.6 0.5 1.0 C20 B:03M1 3.6 0.8 1.0 CD1 A:ILE61 3.9 79.0 1.0 CG A:LEU57 4.0 89.5 1.0 C19 B:03M1 4.0 0.7 1.0 CD2 A:LEU54 4.5 77.8 1.0 CA A:LEU57 4.6 86.5 1.0 N A:GLY58 4.7 99.9 1.0 CL A:03M1 4.7 0.3 1.0 C A:LEU57 4.7 91.2 1.0 CD2 A:LEU57 4.8 90.0 1.0 CG2 A:ILE99 4.9 80.5 1.0 O A:LEU54 4.9 87.9 1.0

Fluorine binding site 5 out of 8 in the Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443 within 5.0Å range: probe atom residue distance (Å) B Occ C:F1 b:94.4 occ:1.00 F25 C:03M1 0.0 94.4 1.0 C23 C:03M1 1.3 91.9 1.0 C24 C:03M1 2.3 0.7 1.0 C22 C:03M1 2.4 0.6 1.0 F26 C:03M1 2.7 0.6 1.0 CG1 D:VAL93 3.1 88.3 1.0 C19 C:03M1 3.6 0.9 1.0 CD1 D:ILE99 3.6 82.7 1.0 C21 C:03M1 3.7 99.1 1.0 CB D:VAL93 3.7 98.0 1.0 CE1 D:PHE91 3.8 70.1 1.0 CG2 D:ILE99 4.0 89.3 1.0 C20 C:03M1 4.1 89.7 1.0 CA D:VAL93 4.2 92.6 1.0 O D:HOH7 4.3 96.7 1.0 CG1 D:ILE99 4.5 88.1 1.0 CD1 D:PHE91 4.6 78.7 1.0 CZ D:PHE91 4.7 72.2 1.0 C18 C:03M1 4.8 0.9 1.0 CB D:ILE99 4.9 0.9 1.0

Fluorine binding site 6 out of 8 in the Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443 within 5.0Å range: probe atom residue distance (Å) B Occ C:F1 b:0.6 occ:1.00 F26 C:03M1 0.0 0.6 1.0 C22 C:03M1 1.4 0.6 1.0 C23 C:03M1 2.3 91.9 1.0 C21 C:03M1 2.4 99.1 1.0 F25 C:03M1 2.7 94.4 1.0 CB D:LEU57 3.5 79.3 1.0 C24 C:03M1 3.6 0.7 1.0 CD1 D:ILE61 3.6 76.2 1.0 C20 C:03M1 3.7 89.7 1.0 CD1 D:LEU57 3.9 0.8 1.0 C19 C:03M1 4.1 0.9 1.0 CG D:LEU57 4.2 97.7 1.0 CE1 D:PHE91 4.5 70.1 1.0 N D:GLY58 4.5 75.5 1.0 CZ D:PHE91 4.6 72.2 1.0 C D:LEU57 4.7 76.7 1.0 CD2 D:LEU54 4.7 77.2 1.0 CA D:LEU57 4.7 73.0 1.0 CL D:03M1 4.8 0.6 1.0 CD2 D:LEU57 4.8 88.5 1.0 O D:LEU54 4.9 77.1 1.0 CG1 D:ILE61 5.0 84.0 1.0 CG1 D:VAL93 5.0 88.3 1.0

Fluorine binding site 7 out of 8 in the Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443 within 5.0Å range: probe atom residue distance (Å) B Occ D:F1 b:0.2 occ:1.00 F25 D:03M1 0.0 0.2 1.0 C23 D:03M1 1.3 0.3 1.0 C22 D:03M1 2.3 0.2 1.0 C24 D:03M1 2.4 0.8 1.0 F26 D:03M1 2.6 0.7 1.0 CG1 C:VAL93 3.1 74.9 1.0 CB C:VAL93 3.5 89.8 1.0 C19 D:03M1 3.6 0.6 1.0 C21 D:03M1 3.7 0.7 1.0 CD1 C:ILE99 3.7 0.0 1.0 CE1 C:PHE91 3.9 86.2 1.0 CA C:VAL93 4.1 0.0 1.0 C20 D:03M1 4.1 0.2 1.0 O C:HOH110 4.3 0.0 1.0 CZ C:PHE91 4.3 75.4 1.0 CG1 C:ILE99 4.4 0.9 1.0 CG2 C:ILE99 4.6 92.6 1.0 C18 D:03M1 4.8 0.8 1.0 CL C:03M1 4.8 0.4 1.0 CG2 C:VAL93 4.9 81.6 1.0

Fluorine binding site 8 out of 8 in the Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of HDM2 with Dimer Inducing Indolyl Hydantoin Ro-2443 within 5.0Å range: probe atom residue distance (Å) B Occ D:F1 b:0.7 occ:1.00 F26 D:03M1 0.0 0.7 1.0 C22 D:03M1 1.3 0.2 1.0 C23 D:03M1 2.3 0.3 1.0 C21 D:03M1 2.4 0.7 1.0 F25 D:03M1 2.6 0.2 1.0 CD1 C:LEU57 3.5 84.2 1.0 C24 D:03M1 3.6 0.8 1.0 C20 D:03M1 3.6 0.2 1.0 CB C:LEU57 3.8 83.2 1.0 C19 D:03M1 4.0 0.6 1.0 CD1 C:ILE61 4.2 68.5 1.0 CG C:LEU57 4.3 85.4 1.0 CD2 C:LEU54 4.5 90.9 1.0 CZ C:PHE91 4.7 75.4 1.0 CG2 C:ILE99 4.8 92.6 1.0 CA C:LEU54 4.9 91.8 1.0 CD2 C:LEU57 4.9 90.9 1.0 O C:LEU54 4.9 96.3 1.0 CB C:LEU54 4.9 92.4 1.0 CE1 C:PHE91 5.0 86.2 1.0

B.Graves, T.Thompson, M.Xia, C.Janson, C.Lukacs, D.Deo, P.Di Lello, D.Fry, C.Garvie, K.S.Huang, L.Gao, C.Tovar, A.Lovey, J.Wanner, L.T.Vassilev. Activation of the P53 Pathway By Small-Molecule-Induced MDM2 and Mdmx Dimerization. Proc.Natl.Acad.Sci.Usa V. 109 11788 2012.
ISSN: ISSN 0027-8424
PubMed: 22745160
DOI: 10.1073/PNAS.1203789109