Chlorine in PDB 4zgk: Structure of MDM2 with Low Molecular Weight Inhibitor.

The structure of Structure of MDM2 with Low Molecular Weight Inhibitor., PDB code: 4zgk was solved by A.Twarda-Clapa, K.M.Zak, E.M.Wrona, P.Grudnik, G.Dubin, T.A.Holak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.610, 56.550, 97.310, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 24.7

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

Chlorine binding site 1 out of 6 in the Structure of MDM2 with Low Molecular Weight Inhibitor.


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. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:26.2 occ:1.00 CL1 A:4NX201 0.0 26.2 1.0 C40 A:4NX201 1.8 23.2 1.0 C41 A:4NX201 2.8 22.8 1.0 C39 A:4NX201 2.8 22.8 1.0 CD2 A:LEU54 3.5 16.4 1.0 CG2 A:ILE99 3.6 19.4 1.0 CA A:HIS96 3.6 27.5 1.0 CB A:HIS96 3.7 29.1 1.0 CE2 A:TYR100 3.7 23.2 1.0 CD2 A:TYR100 3.7 24.0 1.0 CB A:ILE99 3.7 20.0 1.0 O A:HIS96 3.8 23.9 1.0 CG A:HIS96 3.8 28.5 1.0 CD2 A:HIS96 4.0 26.3 1.0 CD1 A:ILE99 4.1 19.1 1.0 C42 A:4NX201 4.1 24.0 1.0 C38 A:4NX201 4.1 23.0 1.0 CD1 A:LEU54 4.1 18.1 1.0 C A:HIS96 4.2 25.2 1.0 CG A:LEU54 4.4 16.3 1.0 CG1 A:ILE99 4.5 19.2 1.0 ND1 A:HIS96 4.5 31.1 1.0 C37 A:4NX201 4.6 23.7 1.0 N A:TYR100 4.8 22.0 1.0 N A:HIS96 4.8 29.5 1.0 NE2 A:HIS96 4.8 26.4 1.0 CA A:ILE99 4.9 20.5 1.0 O A:HOH313 5.0 16.7 0.5

Chlorine binding site 2 out of 6 in the Structure of MDM2 with Low Molecular Weight Inhibitor.


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. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:22.2 occ:1.00 CL2 A:4NX201 0.0 22.2 1.0 C9 A:4NX201 1.8 20.9 1.0 C8 A:4NX201 2.7 20.8 1.0 C10 A:4NX201 2.8 19.1 1.0 CG2 A:ILE99 3.9 19.4 1.0 C41 A:4NX201 4.0 22.8 1.0 C11 A:4NX201 4.1 20.1 1.0 C7 A:4NX201 4.1 20.0 1.0 CD1 A:ILE61 4.1 15.5 1.0 CE1 A:PHE91 4.2 16.3 1.0 CD2 A:LEU54 4.2 16.4 1.0 CD1 A:ILE99 4.2 19.1 1.0 CB A:LEU57 4.3 14.3 1.0 CD1 A:LEU57 4.4 15.6 1.0 CZ A:PHE91 4.5 17.0 1.0 C6 A:4NX201 4.6 19.6 1.0 C42 A:4NX201 4.6 24.0 1.0 CG1 A:ILE99 4.8 19.2 1.0 C40 A:4NX201 4.9 23.2 1.0 CB A:ILE99 4.9 20.0 1.0

Chlorine binding site 3 out of 6 in the Structure of MDM2 with Low Molecular Weight Inhibitor.


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. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:23.5 occ:1.00 CL3 A:4NX201 0.0 23.5 1.0 C57 A:4NX201 1.8 24.1 1.0 C56 A:4NX201 2.7 22.9 1.0 C58 A:4NX201 2.7 24.4 1.0 O B:HOH362 3.1 29.8 1.0 O B:LYS51 3.3 14.9 1.0 O B:HOH323 3.5 15.8 1.0 CD1 A:PHE55 3.6 18.1 1.0 C B:LYS51 3.7 16.6 1.0 CE1 A:PHE55 3.8 18.5 1.0 CB B:LYS51 3.8 19.5 1.0 C46 A:4NX201 4.0 23.0 1.0 C59 A:4NX201 4.0 24.5 1.0 CB B:PHE55 4.1 14.6 1.0 N B:GLU52 4.1 15.5 1.0 CA B:GLU52 4.3 14.9 1.0 CA B:LYS51 4.4 17.2 1.0 C56 B:4NX201 4.4 16.8 1.0 C45 A:4NX201 4.5 23.1 1.0 CG B:GLU52 4.8 15.8 1.0 O B:HOH329 4.8 35.6 1.0 CG A:PHE55 4.8 17.2 1.0 CG B:LYS51 4.8 20.7 1.0 CE B:LYS51 4.8 21.6 0.5 CG B:PHE55 4.9 14.8 1.0 CD B:LYS51 4.9 20.7 0.5

Chlorine binding site 4 out of 6 in the Structure of MDM2 with Low Molecular Weight Inhibitor.


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. within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:20.6 occ:1.00 CL1 B:4NX201 0.0 20.6 1.0 C40 B:4NX201 1.8 19.2 1.0 C41 B:4NX201 2.7 18.6 1.0 C39 B:4NX201 2.7 17.9 1.0 CD2 B:LEU54 3.6 14.0 1.0 CA B:HIS96 3.6 17.6 1.0 CB B:HIS96 3.6 19.3 1.0 CE2 B:TYR100 3.6 20.8 1.0 CG2 B:ILE99 3.7 16.2 1.0 CD2 B:TYR100 3.7 19.7 1.0 CB B:ILE99 3.7 17.1 1.0 CG B:HIS96 3.8 19.7 1.0 O B:HIS96 3.8 15.7 1.0 C42 B:4NX201 4.0 17.2 1.0 CD2 B:HIS96 4.0 19.8 1.0 C38 B:4NX201 4.0 17.4 1.0 CD1 B:ILE99 4.1 16.3 1.0 CD1 B:LEU54 4.1 15.5 1.0 C B:HIS96 4.1 17.6 1.0 ND1 B:HIS96 4.4 20.4 1.0 CG B:LEU54 4.5 14.7 1.0 CG1 B:ILE99 4.5 16.6 1.0 C37 B:4NX201 4.5 18.1 1.0 NE2 B:HIS96 4.8 19.6 1.0 N B:HIS96 4.8 18.2 1.0 N B:TYR100 4.8 17.6 1.0 O B:HOH335 4.8 24.9 1.0 CA B:ILE99 4.9 17.0 1.0 CZ B:TYR100 4.9 20.1 1.0 CE1 B:HIS96 5.0 20.6 1.0

Chlorine binding site 5 out of 6 in the Structure of MDM2 with Low Molecular Weight Inhibitor.


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. within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:17.6 occ:1.00 CL2 B:4NX201 0.0 17.6 1.0 C9 B:4NX201 1.8 17.5 1.0 C10 B:4NX201 2.7 17.9 1.0 C8 B:4NX201 2.7 17.6 1.0 CG2 B:ILE99 3.9 16.2 1.0 C39 B:4NX201 4.0 17.9 1.0 C11 B:4NX201 4.0 16.5 1.0 CE1 B:PHE91 4.0 12.9 1.0 C7 B:4NX201 4.0 16.9 1.0 CD1 B:ILE61 4.1 18.0 1.0 CD2 B:LEU54 4.2 14.0 1.0 CZ B:PHE91 4.2 13.2 1.0 CD1 B:ILE99 4.3 16.3 1.0 CB B:LEU57 4.3 14.1 1.0 CD1 B:LEU57 4.3 14.3 1.0 C6 B:4NX201 4.5 16.8 1.0 C38 B:4NX201 4.5 17.4 1.0 CG1 B:ILE99 4.8 16.6 1.0 CB B:ILE99 4.9 17.1 1.0 C40 B:4NX201 4.9 19.2 1.0 CG B:LEU57 4.9 14.3 1.0

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


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. within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:20.9 occ:1.00 CL3 B:4NX201 0.0 20.9 1.0 C57 B:4NX201 1.8 17.5 1.0 C58 B:4NX201 2.7 17.5 1.0 C56 B:4NX201 2.7 16.8 1.0 O A:LYS51 3.3 20.4 1.0 CD1 B:PHE55 3.4 15.1 1.0 O A:HOH309 3.5 23.8 1.0 CE1 B:PHE55 3.5 15.3 1.0 C A:LYS51 3.7 20.2 1.0 CB A:PHE55 4.0 16.1 1.0 CB A:LYS51 4.0 23.4 1.0 C46 B:4NX201 4.0 16.9 1.0 C59 B:4NX201 4.0 18.1 1.0 N A:GLU52 4.0 19.4 1.0 CA A:GLU52 4.2 19.1 1.0 CA A:LYS51 4.5 22.5 1.0 C45 B:4NX201 4.5 17.8 1.0 C56 A:4NX201 4.5 22.9 1.0 CG B:PHE55 4.6 14.8 1.0 CG A:GLU52 4.7 20.1 1.0 CG A:PHE55 4.7 17.2 1.0 CZ B:PHE55 4.8 16.2 1.0 CD1 A:PHE55 4.9 18.1 1.0 O B:HOH362 5.0 29.8 1.0

E.Surmiak, A.Twarda-Clapa, K.M.Zak, B.Musielak, M.D.Tomala, K.Kubica, P.Grudnik, M.Madej, M.Jablonski, J.Potempa, J.Kalinowska-Tluscik, A.Domling, G.Dubin, T.A.Holak. A Unique MDM2-Binding Mode of the 3-Pyrrolin-2-One- and 2-Furanone-Based Antagonists of the P53-MDM2 Interaction. Acs Chem. Biol. V. 11 3310 2016.
ISSN: ESSN 1554-8937
PubMed: 27709883
DOI: 10.1021/ACSCHEMBIO.6B00596