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

The structure of Structure of MDM2 with Low Molecular Weight Inhibitor, PDB code: 4zfi was solved by K.M.Zak, A.Twarda-Clapa, 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)	56.78 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.360, 70.250, 96.440, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.3

Pages:

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

Binding sites:

The binding sites of Chlorine atom in the Structure of MDM2 with Low Molecular Weight Inhibitor (pdb code 4zfi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Structure of MDM2 with Low Molecular Weight Inhibitor, PDB code: 4zfi:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 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:23.0 occ:1.00 CL1 A:4NJ201 0.0 23.0 1.0 C9 A:4NJ201 1.8 20.5 1.0 C8 A:4NJ201 2.7 22.2 1.0 C10 A:4NJ201 2.8 19.8 1.0 CG2 A:ILE99 3.8 25.0 1.0 CE2 A:PHE91 3.9 23.6 1.0 C7 A:4NJ201 4.0 21.1 1.0 CD1 A:ILE61 4.0 23.5 1.0 C11 A:4NJ201 4.0 20.9 1.0 CZ A:PHE91 4.1 20.6 1.0 CD2 A:LEU54 4.2 20.7 1.0 CD1 A:ILE99 4.2 22.4 1.0 C41 A:4NJ201 4.2 23.1 1.0 CB A:LEU57 4.3 20.9 1.0 CD1 A:LEU57 4.4 24.2 1.0 C6 A:4NJ201 4.5 20.5 1.0 CG1 A:ILE99 4.7 21.9 1.0 C42 A:4NJ201 4.8 25.8 1.0 CB A:ILE99 4.9 22.1 1.0 CG A:LEU57 5.0 20.7 1.0

Chlorine binding site 2 out of 12 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:24.1 occ:1.00 CL2 A:4NJ201 0.0 24.1 1.0 C40 A:4NJ201 1.8 23.0 1.0 C39 A:4NJ201 2.7 22.0 1.0 C41 A:4NJ201 2.8 23.1 1.0 CG2 A:ILE99 3.7 25.0 1.0 O A:HIS96 3.7 27.1 1.0 CE1 A:TYR100 3.7 25.9 1.0 CB A:ILE99 3.7 22.1 1.0 CD1 A:TYR100 3.7 24.7 1.0 CA A:HIS96 3.7 24.5 1.0 CD2 A:LEU54 3.8 20.7 1.0 CB A:HIS96 3.8 25.6 1.0 CG A:HIS96 3.8 28.0 1.0 CD2 A:HIS96 3.9 27.4 1.0 C38 A:4NJ201 4.0 24.9 1.0 CD1 A:ILE99 4.0 22.4 1.0 C42 A:4NJ201 4.1 25.8 1.0 CD1 A:LEU54 4.1 23.5 1.0 C A:HIS96 4.1 25.8 1.0 CG1 A:ILE99 4.4 21.9 1.0 C37 A:4NJ201 4.6 22.9 1.0 CG A:LEU54 4.6 20.7 1.0 ND1 A:HIS96 4.6 27.8 1.0 N A:TYR100 4.7 23.2 1.0 NE2 A:HIS96 4.7 26.7 1.0 N A:HIS96 4.9 25.9 1.0 CA A:ILE99 4.9 23.7 1.0 O A:HOH340 4.9 31.5 1.0 CZ A:TYR100 5.0 27.3 1.0 CG A:TYR100 5.0 23.4 1.0

Chlorine binding site 3 out of 12 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:27.9 occ:1.00 CL3 A:4NJ201 0.0 27.9 1.0 C57 A:4NJ201 1.8 22.3 1.0 C56 A:4NJ201 2.7 22.4 1.0 C58 A:4NJ201 2.8 24.0 1.0 CD1 A:PHE55 3.4 20.0 1.0 CE1 A:PHE55 3.6 21.5 1.0 C46 A:4NJ201 4.0 21.0 1.0 C59 A:4NJ201 4.1 24.1 1.0 C45 A:4NJ201 4.5 22.6 1.0 CG A:PHE55 4.7 19.0 1.0 O A:HOH342 4.9 17.9 1.0 CZ A:PHE55 5.0 21.1 1.0

Chlorine binding site 4 out of 12 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:26.1 occ:1.00 CL1 B:4NJ201 0.0 26.1 1.0 C9 B:4NJ201 1.8 22.3 1.0 C10 B:4NJ201 2.7 23.6 1.0 C8 B:4NJ201 2.7 22.0 1.0 CG2 B:ILE99 3.8 21.4 1.0 CE2 B:PHE91 3.9 21.5 1.0 CD1 B:ILE61 3.9 19.8 1.0 C7 B:4NJ201 4.0 22.7 1.0 C11 B:4NJ201 4.0 23.2 1.0 CZ B:PHE91 4.1 20.6 1.0 CD1 B:ILE99 4.2 20.9 1.0 CD2 B:LEU54 4.2 25.0 1.0 CB B:LEU57 4.3 21.4 1.0 C41 B:4NJ201 4.3 25.1 1.0 CD1 B:LEU57 4.3 24.2 1.0 C6 B:4NJ201 4.5 21.9 1.0 CG1 B:ILE99 4.7 22.0 1.0 CB B:ILE99 4.9 22.3 1.0 CG B:LEU57 4.9 23.4 1.0 C42 B:4NJ201 4.9 23.9 1.0

Chlorine binding site 5 out of 12 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:24.3 occ:1.00 CL2 B:4NJ201 0.0 24.3 1.0 C40 B:4NJ201 1.8 24.6 1.0 C39 B:4NJ201 2.7 25.6 1.0 C41 B:4NJ201 2.8 25.1 1.0 O B:HIS96 3.7 24.3 1.0 CA B:HIS96 3.7 23.2 1.0 CG2 B:ILE99 3.7 21.4 1.0 CB B:ILE99 3.7 22.3 1.0 CE1 B:TYR100 3.7 23.9 1.0 CD2 B:LEU54 3.7 25.0 1.0 CD1 B:TYR100 3.7 24.7 1.0 CB B:HIS96 3.8 23.6 1.0 CG B:HIS96 3.8 25.1 1.0 CD2 B:HIS96 3.9 25.5 1.0 C38 B:4NJ201 4.0 24.7 1.0 CD1 B:ILE99 4.0 20.9 1.0 C42 B:4NJ201 4.0 23.9 1.0 CD1 B:LEU54 4.1 29.8 1.0 C B:HIS96 4.1 25.4 1.0 CG1 B:ILE99 4.5 22.0 1.0 C37 B:4NJ201 4.5 23.3 1.0 CG B:LEU54 4.5 24.6 1.0 ND1 B:HIS96 4.6 25.8 1.0 NE2 B:HIS96 4.7 28.0 1.0 N B:TYR100 4.8 21.7 1.0 O B:HOH311 4.9 31.0 1.0 N B:HIS96 4.9 23.8 1.0 CA B:ILE99 4.9 23.3 1.0

Chlorine binding site 6 out of 12 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:28.4 occ:1.00 CL3 B:4NJ201 0.0 28.4 1.0 C57 B:4NJ201 1.8 24.3 1.0 C56 B:4NJ201 2.7 24.0 1.0 C58 B:4NJ201 2.7 24.7 1.0 CD1 B:PHE55 3.5 22.1 1.0 CE1 B:PHE55 3.7 24.9 1.0 C46 B:4NJ201 4.0 26.2 1.0 C59 B:4NJ201 4.0 27.5 1.0 C45 B:4NJ201 4.5 26.1 1.0 CG B:PHE55 4.7 20.4 1.0 O B:HOH365 4.9 28.3 1.0 O B:HOH329 5.0 23.3 1.0

Chlorine binding site 7 out of 12 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 7 of Structure of MDM2 with Low Molecular Weight Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl201 b:25.5 occ:1.00 CL1 C:4NJ201 0.0 25.5 1.0 C9 C:4NJ201 1.8 23.9 1.0 C10 C:4NJ201 2.7 20.9 1.0 C8 C:4NJ201 2.8 23.0 1.0 CG2 C:ILE99 3.7 21.5 1.0 C11 C:4NJ201 4.0 24.1 1.0 C7 C:4NJ201 4.0 23.7 1.0 CD1 C:ILE61 4.0 22.6 1.0 C39 C:4NJ201 4.2 24.9 1.0 CD1 C:ILE99 4.2 23.9 1.0 CD2 C:LEU54 4.2 20.8 1.0 CE2 C:PHE91 4.3 22.0 1.0 CB C:LEU57 4.4 20.1 1.0 CD1 C:LEU57 4.5 24.4 1.0 C6 C:4NJ201 4.5 22.4 1.0 CZ C:PHE91 4.5 20.6 1.0 CG1 C:ILE99 4.8 22.1 1.0 C38 C:4NJ201 4.8 27.2 1.0 CB C:ILE99 4.8 22.4 1.0 C40 C:4NJ201 5.0 23.3 1.0

Chlorine binding site 8 out of 12 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 8 of Structure of MDM2 with Low Molecular Weight Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl201 b:25.4 occ:1.00 CL2 C:4NJ201 0.0 25.4 1.0 C40 C:4NJ201 1.8 23.3 1.0 C41 C:4NJ201 2.7 23.4 1.0 C39 C:4NJ201 2.7 24.9 1.0 O C:HIS96 3.6 21.8 1.0 CD2 C:LEU54 3.6 20.8 1.0 CA C:HIS96 3.7 26.1 1.0 CE1 C:TYR100 3.7 25.1 1.0 CG2 C:ILE99 3.7 21.5 1.0 CD1 C:TYR100 3.7 23.0 1.0 CB C:HIS96 3.7 27.1 1.0 CB C:ILE99 3.8 22.4 1.0 CG C:HIS96 3.9 27.9 1.0 CD2 C:HIS96 3.9 28.7 1.0 C42 C:4NJ201 3.9 25.4 1.0 CD1 C:LEU54 4.0 22.8 1.0 C38 C:4NJ201 4.0 27.2 1.0 C C:HIS96 4.1 25.1 1.0 CD1 C:ILE99 4.2 23.9 1.0 CG C:LEU54 4.5 19.6 1.0 C37 C:4NJ201 4.5 24.8 1.0 CG1 C:ILE99 4.6 22.1 1.0 ND1 C:HIS96 4.6 29.9 1.0 NE2 C:HIS96 4.7 30.8 1.0 O C:HOH325 4.8 28.4 1.0 N C:TYR100 4.8 20.7 1.0 N C:HIS96 4.9 25.3 1.0 CA C:ILE99 4.9 19.8 1.0 CZ C:TYR100 4.9 24.7 1.0 CG C:TYR100 5.0 21.2 1.0

Chlorine binding site 9 out of 12 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 9 of Structure of MDM2 with Low Molecular Weight Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl201 b:28.5 occ:1.00 CL3 C:4NJ201 0.0 28.5 1.0 C57 C:4NJ201 1.8 23.6 1.0 C56 C:4NJ201 2.7 22.5 1.0 C58 C:4NJ201 2.8 23.9 1.0 CD1 C:PHE55 3.4 21.2 1.0 CE1 C:PHE55 3.7 23.4 1.0 C46 C:4NJ201 4.0 21.9 1.0 C59 C:4NJ201 4.1 23.1 1.0 C45 C:4NJ201 4.5 22.7 1.0 CG C:PHE55 4.6 19.4 1.0

Chlorine binding site 10 out of 12 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 10 of Structure of MDM2 with Low Molecular Weight Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl201 b:29.0 occ:1.00 CL1 D:4NJ201 0.0 29.0 1.0 C9 D:4NJ201 1.8 25.9 1.0 C8 D:4NJ201 2.7 23.2 1.0 C10 D:4NJ201 2.7 25.4 1.0 CG2 D:ILE99 3.9 21.6 1.0 CD1 D:ILE61 4.0 23.5 1.0 C7 D:4NJ201 4.0 26.1 1.0 C11 D:4NJ201 4.0 24.4 1.0 C41 D:4NJ201 4.1 21.4 1.0 CD1 D:ILE99 4.2 21.7 1.0 CE2 D:PHE91 4.2 20.8 1.0 CD2 D:LEU54 4.4 21.3 1.0 CB D:LEU57 4.4 25.1 1.0 CZ D:PHE91 4.5 22.4 1.0 C6 D:4NJ201 4.5 26.3 1.0 CD1 D:LEU57 4.6 29.6 1.0 CG1 D:ILE99 4.8 21.1 1.0 C42 D:4NJ201 4.8 23.9 1.0 CB D:ILE99 4.9 19.6 1.0 C40 D:4NJ201 5.0 23.2 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