Chlorine in PDB 5j7f: Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker.

The structure of Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker., PDB code: 5j7f was solved by A.Twarda-Clapa, K.Kubica, K.Guzik, G.Dubin, T.A.Holak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	87.38 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.758, 174.750, 37.810, 90.00, 93.48, 90.00
R / Rfree (%)	18.3 / 24.2

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

Fluorine

(F)

4 atoms

The binding sites of Chlorine atom in the Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker. (pdb code 5j7f). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker., PDB code: 5j7f:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in the Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:29.3 occ:1.00 CL1 A:6GG201 0.0 29.3 1.0 C57 A:6GG201 1.8 22.7 1.0 C58 A:6GG201 2.7 25.1 1.0 C56 A:6GG201 2.8 24.1 1.0 CG2 A:ILE99 3.7 29.8 1.0 CD1 A:ILE61 3.8 26.7 1.0 CZ A:PHE86 3.9 29.1 1.0 CE2 A:PHE86 3.9 28.9 1.0 CB A:LEU57 4.0 27.1 1.0 C59 A:6GG201 4.0 23.6 1.0 C46 A:6GG201 4.0 24.7 1.0 CD1 A:LEU57 4.1 27.2 1.0 CZ A:PHE91 4.1 29.9 1.0 CD1 A:LEU54 4.4 29.1 1.0 CE2 A:PHE91 4.4 30.2 1.0 C45 A:6GG201 4.5 24.1 1.0 CG A:LEU57 4.6 26.8 1.0 CD1 A:ILE99 4.6 29.5 1.0 CG1 A:ILE99 4.7 29.6 1.0 CD1 A:ILE103 4.8 25.8 1.0 CB A:ILE99 4.9 29.3 1.0 CD2 A:LEU57 4.9 26.6 1.0

Chlorine binding site 2 out of 8 in the Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:34.1 occ:1.00 CL2 A:6GG201 0.0 34.1 1.0 C9 A:6GG201 1.8 33.2 1.0 C10 A:6GG201 2.7 36.0 1.0 C8 A:6GG201 2.7 32.8 1.0 CD1 A:LEU54 3.5 29.1 1.0 CB A:HIS96 3.7 31.1 1.0 CG A:HIS96 3.7 32.8 1.0 CE1 A:TYR100 3.8 31.1 1.0 CA A:HIS96 3.8 30.4 1.0 O A:HIS96 3.8 30.3 1.0 CD1 A:TYR100 3.8 30.9 1.0 CG2 A:ILE99 4.0 29.8 1.0 C11 A:6GG201 4.0 37.8 1.0 CB A:ILE99 4.0 29.3 1.0 C7 A:6GG201 4.0 36.5 1.0 CD2 A:HIS96 4.0 32.2 1.0 CG A:LEU54 4.2 28.7 1.0 ND1 A:HIS96 4.2 33.2 1.0 CD1 A:ILE99 4.2 29.5 1.0 C A:HIS96 4.3 30.4 1.0 CG2 A:THR16 4.4 36.0 1.0 C6 A:6GG201 4.5 35.3 1.0 NE2 A:HIS96 4.7 33.6 1.0 CG1 A:ILE99 4.7 29.6 1.0 CE1 A:HIS96 4.7 33.0 1.0 CB A:THR16 5.0 37.0 1.0

Chlorine binding site 3 out of 8 in the Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker. within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:31.3 occ:1.00 CL1 B:6GG201 0.0 31.3 1.0 C57 B:6GG201 1.8 33.1 1.0 C56 B:6GG201 2.7 32.4 1.0 C58 B:6GG201 2.7 33.2 1.0 CB B:LEU57 3.8 30.5 1.0 CG2 B:ILE99 3.8 27.6 1.0 CD1 B:ILE61 3.9 29.6 1.0 CD1 B:LEU57 3.9 30.4 1.0 C46 B:6GG201 4.0 33.8 1.0 C59 B:6GG201 4.0 33.3 1.0 CZ B:PHE91 4.1 31.1 1.0 CD1 B:LEU54 4.2 31.9 1.0 CE2 B:PHE86 4.2 32.7 1.0 CZ B:PHE86 4.2 33.1 1.0 CE2 B:PHE91 4.2 31.4 1.0 CG B:LEU57 4.5 31.3 1.0 C45 B:6GG201 4.5 34.7 1.0 CG1 B:ILE99 4.8 29.2 1.0 CD1 B:ILE99 4.8 31.7 1.0 CB B:ILE99 4.9 28.1 1.0

Chlorine binding site 4 out of 8 in the Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker. within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:39.5 occ:1.00 CL2 B:6GG201 0.0 39.5 1.0 C9 B:6GG201 1.8 41.4 1.0 C10 B:6GG201 2.7 33.7 1.0 C8 B:6GG201 2.7 39.2 1.0 CD1 B:LEU54 3.5 31.9 1.0 CG B:HIS96 3.7 34.2 1.0 CB B:HIS96 3.8 34.3 1.0 CG2 B:ILE99 3.8 27.6 1.0 CA B:HIS96 3.8 33.2 1.0 O B:HIS96 3.8 31.7 1.0 CB B:ILE99 3.9 28.1 1.0 CD1 B:TYR100 3.9 31.4 1.0 CE1 B:TYR100 3.9 32.8 1.0 C11 B:6GG201 4.0 36.1 1.0 C7 B:6GG201 4.0 38.7 1.0 CD2 B:HIS96 4.1 33.4 1.0 ND1 B:HIS96 4.1 35.7 1.0 CG B:LEU54 4.2 32.2 1.0 CD1 B:ILE99 4.2 31.7 1.0 C B:HIS96 4.3 32.4 1.0 CG2 B:THR16 4.5 59.1 1.0 C6 B:6GG201 4.5 34.7 1.0 NE2 B:HIS96 4.6 35.6 1.0 CE1 B:HIS96 4.7 36.1 1.0 CG1 B:ILE99 4.7 29.2 1.0 N B:TYR100 4.9 27.9 1.0 CD2 B:LEU54 5.0 33.1 1.0

Chlorine binding site 5 out of 8 in the Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker. within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl201 b:35.1 occ:1.00 CL1 C:6GG201 0.0 35.1 1.0 C57 C:6GG201 1.8 31.0 1.0 C56 C:6GG201 2.7 29.6 1.0 C58 C:6GG201 2.7 29.3 1.0 CD1 C:ILE61 3.9 28.7 1.0 CG2 C:ILE99 3.9 28.5 1.0 CB C:LEU57 4.0 31.6 1.0 CE2 C:PHE86 4.0 34.0 1.0 CZ C:PHE86 4.0 34.3 1.0 C46 C:6GG201 4.0 31.0 1.0 CD1 C:LEU57 4.0 32.8 1.0 C59 C:6GG201 4.0 30.4 1.0 CZ C:PHE91 4.1 30.5 1.0 CE2 C:PHE91 4.4 31.0 1.0 CD1 C:LEU54 4.4 30.0 1.0 C45 C:6GG201 4.5 29.0 1.0 CG C:LEU57 4.5 33.4 1.0 CD1 C:ILE99 4.8 30.0 1.0 CG1 C:ILE99 4.8 29.6 1.0 CD1 C:ILE103 4.9 31.5 1.0

Chlorine binding site 6 out of 8 in the Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker. within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl201 b:39.4 occ:1.00 CL2 C:6GG201 0.0 39.4 1.0 C9 C:6GG201 1.8 40.9 1.0 C10 C:6GG201 2.8 36.4 1.0 C8 C:6GG201 2.8 32.6 1.0 CB C:HIS96 3.6 31.7 1.0 CG C:HIS96 3.7 31.3 1.0 CD1 C:LEU54 3.7 30.0 1.0 CA C:HIS96 3.8 31.1 1.0 CD1 C:TYR100 3.8 30.3 1.0 CE1 C:TYR100 3.9 31.3 1.0 CG2 C:ILE99 3.9 28.5 1.0 CD2 C:HIS96 4.0 31.3 1.0 C7 C:6GG201 4.1 37.6 1.0 C11 C:6GG201 4.1 36.9 1.0 O C:HIS96 4.1 32.4 1.0 CB C:ILE99 4.1 28.4 1.0 CG C:LEU54 4.2 31.1 1.0 CD1 C:ILE99 4.2 30.0 1.0 ND1 C:HIS96 4.2 31.3 1.0 C C:HIS96 4.4 31.4 1.0 CG2 C:THR16 4.5 40.1 1.0 C6 C:6GG201 4.6 38.4 1.0 NE2 C:HIS96 4.7 32.8 1.0 CE1 C:HIS96 4.8 31.4 1.0 CG1 C:ILE99 4.8 29.6 1.0 N C:HIS96 5.0 31.5 1.0

Chlorine binding site 7 out of 8 in the Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker. within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl201 b:32.2 occ:1.00 CL1 D:6GG201 0.0 32.2 1.0 C57 D:6GG201 1.8 28.6 1.0 C58 D:6GG201 2.7 30.1 1.0 C56 D:6GG201 2.7 27.2 1.0 CG2 D:ILE99 3.8 26.1 1.0 CD1 D:ILE61 3.8 30.7 1.0 CD1 D:LEU57 3.9 33.5 1.0 CB D:LEU57 3.9 33.4 1.0 CE2 D:PHE86 4.0 34.5 1.0 C46 D:6GG201 4.0 27.9 1.0 C59 D:6GG201 4.0 28.5 1.0 CZ D:PHE91 4.0 30.1 1.0 CZ D:PHE86 4.0 34.2 1.0 CE2 D:PHE91 4.2 30.4 1.0 CD1 D:LEU54 4.3 38.2 1.0 C45 D:6GG201 4.5 30.1 1.0 CG D:LEU57 4.5 34.5 1.0 CD1 D:ILE99 4.6 27.9 1.0 CG1 D:ILE99 4.9 27.9 1.0 CB D:ILE99 5.0 27.1 1.0

Chlorine binding site 8 out of 8 in the Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of MDM2 with Low Molecular Weight Inhibitor with Aliphatic Linker. within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl201 b:38.5 occ:1.00 CL2 D:6GG201 0.0 38.5 1.0 C9 D:6GG201 1.8 43.0 1.0 C10 D:6GG201 2.7 42.8 1.0 C8 D:6GG201 2.8 39.3 1.0 CB D:HIS96 3.6 36.7 1.0 CA D:HIS96 3.6 33.9 1.0 CG D:HIS96 3.7 40.3 1.0 CD1 D:LEU54 3.7 38.2 1.0 O D:HIS96 3.7 32.2 1.0 CG2 D:ILE99 3.9 26.1 1.0 CB D:ILE99 3.9 27.1 1.0 CE1 D:TYR100 3.9 34.1 1.0 CD1 D:TYR100 3.9 35.2 1.0 CD1 D:ILE99 4.0 27.9 1.0 C11 D:6GG201 4.0 40.3 1.0 C7 D:6GG201 4.0 36.9 1.0 CD2 D:HIS96 4.1 44.1 1.0 CG D:LEU54 4.1 37.8 1.0 C D:HIS96 4.1 34.1 1.0 ND1 D:HIS96 4.2 45.0 1.0 CG1 D:ILE99 4.5 27.9 1.0 C6 D:6GG201 4.5 39.3 1.0 CG2 D:THR16 4.6 70.2 1.0 CD2 D:LEU54 4.6 40.2 1.0 NE2 D:HIS96 4.8 42.6 1.0 CE1 D:HIS96 4.8 45.6 1.0 O D:HOH309 4.8 37.1 1.0 N D:HIS96 4.8 34.1 1.0 N D:TYR100 5.0 32.7 1.0

A.Twarda-Clapa, S.Krzanik, K.Kubica, K.Guzik, B.Labuzek, C.G.Neochoritis, K.Khoury, K.Kowalska, M.Czub, G.Dubin, A.Domling, L.Skalniak, T.A.Holak. 1,4,5-Trisubstituted Imidazole-Based P53-MDM2/Mdmx Antagonists with Aliphatic Linkers For Conjugation with Biological Carriers. J. Med. Chem. V. 60 4234 2017.
ISSN: ISSN 1520-4804
PubMed: 28482147
DOI: 10.1021/ACS.JMEDCHEM.7B00104