Fluorine in PDB 5hmk: HDM2 in Complex with A 3,3-Disubstituted Piperidine

The structure of HDM2 in Complex with A 3,3-Disubstituted Piperidine, PDB code: 5hmk was solved by G.Scapin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.75 / 2.17
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.160, 39.510, 133.560, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 26.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the HDM2 in Complex with A 3,3-Disubstituted Piperidine (pdb code 5hmk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the HDM2 in Complex with A 3,3-Disubstituted Piperidine, PDB code: 5hmk:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in the HDM2 in Complex with A 3,3-Disubstituted Piperidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of HDM2 in Complex with A 3,3-Disubstituted Piperidine within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:55.8 occ:1.00 F1 A:62Q1001 0.0 55.8 1.0 C35 A:62Q1001 1.3 58.3 1.0 F3 A:62Q1001 2.1 59.6 1.0 F2 A:62Q1001 2.2 60.7 1.0 C10 A:62Q1001 2.4 55.4 1.0 C9 A:62Q1001 3.2 57.8 1.0 CD1 A:ILE61 3.3 59.2 1.0 CB A:LEU57 3.4 53.4 1.0 C11 A:62Q1001 3.4 52.3 1.0 CD1 A:LEU57 3.8 56.1 1.0 CG A:LEU57 3.9 56.7 1.0 CZ A:PHE91 4.0 54.5 1.0 CD2 A:LEU57 4.1 60.1 1.0 CZ A:PHE86 4.1 54.4 1.0 CE2 A:PHE86 4.1 56.8 1.0 C A:LEU57 4.3 57.3 1.0 O A:LEU57 4.3 56.4 1.0 CA A:LEU57 4.4 54.0 1.0 CE1 A:PHE91 4.5 54.8 1.0 C8 A:62Q1001 4.5 56.3 1.0 CG1 A:ILE61 4.5 59.2 1.0 CD2 A:LEU82 4.5 60.4 1.0 C12 A:62Q1001 4.6 51.6 1.0 N A:GLY58 4.8 54.4 1.0 CD1 A:LEU82 4.9 58.7 1.0

Fluorine binding site 2 out of 12 in the HDM2 in Complex with A 3,3-Disubstituted Piperidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of HDM2 in Complex with A 3,3-Disubstituted Piperidine within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:60.7 occ:1.00 F2 A:62Q1001 0.0 60.7 1.0 C35 A:62Q1001 1.4 58.3 1.0 F1 A:62Q1001 2.2 55.8 1.0 F3 A:62Q1001 2.3 59.6 1.0 C10 A:62Q1001 2.3 55.4 1.0 C9 A:62Q1001 2.8 57.8 1.0 CE1 A:PHE91 3.2 54.8 1.0 CG2 A:ILE99 3.3 56.9 1.0 CZ A:PHE91 3.4 54.5 1.0 C11 A:62Q1001 3.5 52.3 1.0 CD1 A:ILE99 3.8 60.9 1.0 CG1 A:ILE99 3.9 58.8 1.0 CE2 A:PHE86 4.0 56.8 1.0 C8 A:62Q1001 4.2 56.3 1.0 CB A:ILE99 4.2 58.0 1.0 CZ A:PHE86 4.3 54.4 1.0 CD1 A:PHE91 4.4 55.6 1.0 CD1 A:ILE61 4.5 59.2 1.0 CE2 A:PHE91 4.7 57.4 1.0 C12 A:62Q1001 4.7 51.6 1.0 C7 A:62Q1001 4.9 53.6 1.0 CD2 A:LEU54 5.0 61.1 1.0

Fluorine binding site 3 out of 12 in the HDM2 in Complex with A 3,3-Disubstituted Piperidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of HDM2 in Complex with A 3,3-Disubstituted Piperidine within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:59.6 occ:1.00 F3 A:62Q1001 0.0 59.6 1.0 C35 A:62Q1001 1.4 58.3 1.0 F1 A:62Q1001 2.1 55.8 1.0 F2 A:62Q1001 2.3 60.7 1.0 C10 A:62Q1001 2.4 55.4 1.0 C11 A:62Q1001 2.7 52.3 1.0 CD1 A:LEU57 3.3 56.1 1.0 CB A:LEU57 3.4 53.4 1.0 CD2 A:LEU54 3.6 61.1 1.0 C9 A:62Q1001 3.7 57.8 1.0 CD1 A:ILE103 3.9 48.7 1.0 CG2 A:ILE99 3.9 56.9 1.0 CG A:LEU57 3.9 56.7 1.0 C12 A:62Q1001 4.1 51.6 1.0 CA A:LEU54 4.2 53.7 1.0 O A:LEU54 4.3 54.8 1.0 CZ A:PHE86 4.4 54.4 1.0 CG1 A:ILE103 4.7 53.2 1.0 CD2 A:LEU57 4.7 60.1 1.0 CB A:LEU54 4.7 53.1 1.0 CG A:LEU54 4.7 57.6 1.0 CE2 A:PHE86 4.8 56.8 1.0 C A:LEU54 4.8 56.5 1.0 CA A:LEU57 4.8 54.0 1.0 C8 A:62Q1001 4.8 56.3 1.0 C A:LEU57 5.0 57.3 1.0 C7 A:62Q1001 5.0 53.6 1.0

Fluorine binding site 4 out of 12 in the HDM2 in Complex with A 3,3-Disubstituted Piperidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of HDM2 in Complex with A 3,3-Disubstituted Piperidine within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:60.3 occ:1.00 F4 A:62Q1001 0.0 60.3 1.0 C36 A:62Q1001 1.4 59.3 1.0 F6 A:62Q1001 2.2 61.8 1.0 F5 A:62Q1001 2.2 58.0 1.0 C18 A:62Q1001 2.5 57.9 1.0 O A:GLN72 3.0 75.8 1.0 O3 A:62Q1001 3.2 54.5 1.0 C14 A:62Q1001 3.3 58.0 1.0 C13 A:62Q1001 3.4 58.2 1.0 C17 A:62Q1001 3.4 57.5 1.0 CB A:VAL93 3.8 63.0 1.0 CG2 A:VAL93 3.8 62.5 1.0 CG2 A:VAL75 4.2 65.3 1.0 C A:GLN72 4.2 77.7 1.0 CG1 A:VAL93 4.2 63.3 1.0 N1 A:62Q1001 4.4 58.0 1.0 CA A:HIS73 4.4 72.6 1.0 C8 A:62Q1001 4.5 56.3 1.0 C A:HIS73 4.5 74.0 1.0 C15 A:62Q1001 4.5 56.8 1.0 O A:HIS73 4.5 72.5 1.0 C16 A:62Q1001 4.7 57.1 1.0 N A:HIS73 4.8 73.7 1.0 O2 A:62Q1001 4.8 56.2 1.0

Fluorine binding site 5 out of 12 in the HDM2 in Complex with A 3,3-Disubstituted Piperidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of HDM2 in Complex with A 3,3-Disubstituted Piperidine within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:58.0 occ:1.00 F5 A:62Q1001 0.0 58.0 1.0 C36 A:62Q1001 1.4 59.3 1.0 F6 A:62Q1001 2.2 61.8 1.0 F4 A:62Q1001 2.2 60.3 1.0 C18 A:62Q1001 2.4 57.9 1.0 C14 A:62Q1001 3.0 58.0 1.0 C13 A:62Q1001 3.0 58.2 1.0 C8 A:62Q1001 3.4 56.3 1.0 N1 A:62Q1001 3.4 58.0 1.0 O2 A:62Q1001 3.5 56.2 1.0 O3 A:62Q1001 3.5 54.5 1.0 C3 A:62Q1001 3.5 55.3 1.0 C17 A:62Q1001 3.6 57.5 1.0 CG2 A:ILE61 3.7 56.9 1.0 C2 A:62Q1001 3.7 54.0 1.0 C7 A:62Q1001 3.9 53.6 1.0 C15 A:62Q1001 4.3 56.8 1.0 CG2 A:VAL75 4.4 65.3 1.0 C9 A:62Q1001 4.4 57.8 1.0 C4 A:62Q1001 4.4 54.2 1.0 CG2 A:VAL93 4.5 62.5 1.0 C5 A:62Q1001 4.5 57.5 1.0 CB A:ILE61 4.6 58.6 1.0 C1 A:62Q1001 4.7 56.0 1.0 SD A:MET62 4.7 61.2 1.0 C16 A:62Q1001 4.8 57.1 1.0 CD1 A:ILE61 4.8 59.2 1.0 O A:GLN72 5.0 75.8 1.0

Fluorine binding site 6 out of 12 in the HDM2 in Complex with A 3,3-Disubstituted Piperidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of HDM2 in Complex with A 3,3-Disubstituted Piperidine within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:61.8 occ:1.00 F6 A:62Q1001 0.0 61.8 1.0 C36 A:62Q1001 1.4 59.3 1.0 F4 A:62Q1001 2.2 60.3 1.0 F5 A:62Q1001 2.2 58.0 1.0 C18 A:62Q1001 2.3 57.9 1.0 C17 A:62Q1001 2.6 57.5 1.0 CB A:TYR67 3.5 63.4 1.0 CG2 A:ILE61 3.5 56.9 1.0 CG A:TYR67 3.6 63.0 1.0 C14 A:62Q1001 3.7 58.0 1.0 O A:GLN72 3.7 75.8 1.0 CD1 A:TYR67 3.7 63.6 1.0 CG2 A:VAL75 3.8 65.3 1.0 C16 A:62Q1001 4.0 57.1 1.0 CD2 A:TYR67 4.4 64.4 1.0 C13 A:62Q1001 4.4 58.2 1.0 CE1 A:TYR67 4.5 65.2 1.0 C15 A:62Q1001 4.7 56.8 1.0 O3 A:62Q1001 4.7 54.5 1.0 O A:LEU66 4.8 67.1 1.0 N3 A:62Q1001 4.9 56.7 1.0 C A:GLN72 4.9 77.7 1.0 CA A:TYR67 4.9 64.9 1.0 CB A:ILE61 4.9 58.6 1.0 SD A:MET62 5.0 61.2 1.0

Fluorine binding site 7 out of 12 in the HDM2 in Complex with A 3,3-Disubstituted Piperidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of HDM2 in Complex with A 3,3-Disubstituted Piperidine within 5.0Å range: probe atom residue distance (Å) B Occ B:F1001 b:44.0 occ:1.00 F1 B:62Q1001 0.0 44.0 1.0 C35 B:62Q1001 1.3 43.8 1.0 F3 B:62Q1001 2.1 44.0 1.0 F2 B:62Q1001 2.2 45.1 1.0 C10 B:62Q1001 2.4 42.5 1.0 CD1 B:ILE61 3.2 43.6 1.0 C9 B:62Q1001 3.2 41.3 1.0 C11 B:62Q1001 3.4 37.6 1.0 CB B:LEU57 3.5 41.4 1.0 CZ B:PHE91 3.8 42.4 1.0 CD1 B:LEU57 4.0 45.0 1.0 CE2 B:PHE86 4.1 39.8 1.0 CE1 B:PHE91 4.2 42.9 1.0 CG B:LEU57 4.2 45.5 1.0 CZ B:PHE86 4.3 37.5 1.0 CG1 B:ILE61 4.4 44.2 1.0 C B:LEU57 4.5 46.3 1.0 C8 B:62Q1001 4.5 42.8 1.0 O B:LEU57 4.6 46.8 1.0 C12 B:62Q1001 4.6 40.3 1.0 CD2 B:LEU57 4.6 49.4 1.0 CA B:LEU57 4.6 42.4 1.0 CD2 B:LEU82 4.7 42.2 1.0 CE2 B:PHE91 4.8 44.0 1.0 CG2 B:ILE99 4.9 41.4 1.0 N B:GLY58 4.9 40.9 1.0 CD1 B:LEU82 5.0 41.3 1.0

Fluorine binding site 8 out of 12 in the HDM2 in Complex with A 3,3-Disubstituted Piperidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of HDM2 in Complex with A 3,3-Disubstituted Piperidine within 5.0Å range: probe atom residue distance (Å) B Occ B:F1001 b:45.1 occ:1.00 F2 B:62Q1001 0.0 45.1 1.0 C35 B:62Q1001 1.3 43.8 1.0 F3 B:62Q1001 2.1 44.0 1.0 F1 B:62Q1001 2.2 44.0 1.0 C10 B:62Q1001 2.4 42.5 1.0 C9 B:62Q1001 2.9 41.3 1.0 CE1 B:PHE91 3.2 42.9 1.0 CG2 B:ILE99 3.2 41.4 1.0 CZ B:PHE91 3.5 42.4 1.0 C11 B:62Q1001 3.6 37.6 1.0 CD1 B:ILE99 3.8 43.5 1.0 CG1 B:ILE99 3.8 41.7 1.0 CB B:ILE99 4.1 41.6 1.0 C8 B:62Q1001 4.2 42.8 1.0 CE2 B:PHE86 4.3 39.8 1.0 CD1 B:PHE91 4.4 43.6 1.0 CD1 B:ILE61 4.6 43.6 1.0 C12 B:62Q1001 4.7 40.3 1.0 CZ B:PHE86 4.7 37.5 1.0 CE2 B:PHE91 4.7 44.0 1.0 C24 B:62Q1001 4.8 40.2 1.0 CD2 B:LEU54 4.9 42.8 1.0 C7 B:62Q1001 4.9 44.2 1.0 C25 B:62Q1001 5.0 39.9 1.0

Fluorine binding site 9 out of 12 in the HDM2 in Complex with A 3,3-Disubstituted Piperidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of HDM2 in Complex with A 3,3-Disubstituted Piperidine within 5.0Å range: probe atom residue distance (Å) B Occ B:F1001 b:44.0 occ:1.00 F3 B:62Q1001 0.0 44.0 1.0 C35 B:62Q1001 1.3 43.8 1.0 F1 B:62Q1001 2.1 44.0 1.0 F2 B:62Q1001 2.1 45.1 1.0 C10 B:62Q1001 2.4 42.5 1.0 C11 B:62Q1001 2.8 37.6 1.0 CD2 B:LEU54 3.4 42.8 1.0 CD1 B:LEU57 3.5 45.0 1.0 C9 B:62Q1001 3.7 41.3 1.0 CB B:LEU57 3.7 41.4 1.0 CG2 B:ILE99 3.7 41.4 1.0 CD1 B:ILE103 4.0 41.5 1.0 C12 B:62Q1001 4.2 40.3 1.0 CG B:LEU57 4.2 45.5 1.0 CA B:LEU54 4.3 39.5 1.0 O B:LEU54 4.4 44.5 1.0 CG B:LEU54 4.7 42.2 1.0 CZ B:PHE86 4.7 37.5 1.0 CB B:LEU54 4.7 39.2 1.0 CE2 B:PHE86 4.8 39.8 1.0 C8 B:62Q1001 4.8 42.8 1.0 C B:LEU54 4.9 44.9 1.0 C24 B:62Q1001 4.9 40.2 1.0 CG1 B:ILE103 4.9 38.9 1.0 CD1 B:ILE61 5.0 43.6 1.0

Fluorine binding site 10 out of 12 in the HDM2 in Complex with A 3,3-Disubstituted Piperidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of HDM2 in Complex with A 3,3-Disubstituted Piperidine within 5.0Å range: probe atom residue distance (Å) B Occ B:F1001 b:52.0 occ:1.00 F4 B:62Q1001 0.0 52.0 1.0 C36 B:62Q1001 1.4 50.1 1.0 F5 B:62Q1001 2.1 48.2 1.0 F6 B:62Q1001 2.2 52.0 1.0 C18 B:62Q1001 2.4 49.4 1.0 O3 B:62Q1001 2.8 52.9 1.0 C13 B:62Q1001 3.0 48.6 1.0 C14 B:62Q1001 3.0 49.4 1.0 O B:GLN72 3.2 55.0 1.0 CG2 B:VAL93 3.3 51.4 1.0 C17 B:62Q1001 3.6 49.0 1.0 CG1 B:VAL93 4.0 53.4 1.0 N1 B:62Q1001 4.0 45.0 1.0 CB B:VAL93 4.0 52.2 1.0 C8 B:62Q1001 4.1 42.8 1.0 O2 B:62Q1001 4.2 48.0 1.0 C15 B:62Q1001 4.4 49.1 1.0 C B:GLN72 4.4 58.5 1.0 CG2 B:VAL75 4.7 46.2 1.0 C16 B:62Q1001 4.7 50.3 1.0 C3 B:62Q1001 4.7 47.8 1.0 C7 B:62Q1001 4.7 44.2 1.0 C4 B:62Q1001 4.9 44.5 1.0

S.L.Bogen, W.Pan, C.R.Gibeau, B.R.Lahue, Y.Ma, L.G.Nair, E.Seigel, G.W.Shipps, Y.Tian, Y.Wang, Y.Lin, M.Liu, S.Liu, A.Mirza, X.Wang, P.Lipari, C.Seidel-Dugan, D.J.Hicklin, W.R.Bishop, D.Rindgen, A.Nomeir, W.Prosise, P.Reichert, G.Scapin, C.Strickland, R.J.Doll. Discovery of Novel 3,3-Disubstituted Piperidines As Orally Bioavailable, Potent, and Efficacious HDM2-P53 Inhibitors. Acs Med.Chem.Lett. V. 7 324 2016.
ISSN: ISSN 1948-5875
PubMed: 26985323
DOI: 10.1021/ACSMEDCHEMLETT.5B00472