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Chlorine in PDB 8pwc: Crystal Structure of MDM2 with Brigimadlin

Enzymatic activity of Crystal Structure of MDM2 with Brigimadlin

All present enzymatic activity of Crystal Structure of MDM2 with Brigimadlin:
2.3.2.27;

Protein crystallography data

The structure of Crystal Structure of MDM2 with Brigimadlin, PDB code: 8pwc was solved by G.Bader, B.Wolkerstorfer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.60 / 1.46
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 83.207, 83.207, 42.056, 90, 90, 120
R / Rfree (%) 19.9 / 22.6

Other elements in 8pwc:

The structure of Crystal Structure of MDM2 with Brigimadlin also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of MDM2 with Brigimadlin (pdb code 8pwc). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of MDM2 with Brigimadlin, PDB code: 8pwc:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 8pwc

Go back to Chlorine Binding Sites List in 8pwc
Chlorine binding site 1 out of 6 in the Crystal Structure of MDM2 with Brigimadlin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of MDM2 with Brigimadlin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:20.8
occ:1.00
 CL12 A:G7I201 0.0 20.8 1.0
C4 A:G7I201 1.7 18.8 1.0
C3 A:G7I201 2.7 17.9 1.0
C5 A:G7I201 2.7 17.6 1.0
H3 A:G7I201 2.8 18.0 1.0
H5 A:G7I201 2.8 17.7 1.0
HB3 A:LEU57 2.9 18.4 1.0
HZ A:PHE86 2.9 25.0 1.0
HD11 A:ILE61 3.2 21.3 1.0
HD13 A:LEU57 3.2 22.5 1.0
HD12 A:LEU57 3.3 22.5 1.0
HG21 A:ILE99 3.3 20.9 1.0
HE2 A:PHE86 3.4 26.7 1.0
HB2 A:LEU57 3.4 18.4 1.0
HD11 A:ILE103 3.5 20.9 1.0
HD23 A:LEU54 3.5 24.0 1.0
CB A:LEU57 3.6 18.4 1.0
CD1 A:LEU57 3.7 22.5 1.0
HG23 A:ILE99 3.7 20.9 1.0
CZ A:PHE86 3.8 25.0 1.0
C8 A:G7I201 4.0 17.8 1.0
C6 A:G7I201 4.0 17.9 1.0
CE2 A:PHE86 4.0 26.7 1.0
HD11 A:LEU82 4.0 28.8 1.0
CG2 A:ILE99 4.0 20.9 1.0
HD12 A:ILE61 4.0 21.3 1.0
CD1 A:ILE61 4.1 21.3 1.0
HZ A:PHE91 4.1 24.8 1.0
CG A:LEU57 4.3 20.4 1.0
CD2 A:LEU54 4.3 24.0 1.0
HD22 A:LEU54 4.4 24.0 1.0
HD13 A:ILE99 4.4 21.5 1.0
C7 A:G7I201 4.5 17.5 1.0
HG22 A:ILE99 4.5 20.8 1.0
HD21 A:LEU82 4.5 27.8 1.0
HD13 A:ILE61 4.5 21.2 1.0
CD1 A:ILE103 4.5 21.0 1.0
HA A:LEU54 4.5 16.9 1.0
HE1 A:PHE91 4.6 24.4 1.0
HD22 A:LEU57 4.6 22.0 1.0
HD21 A:LEU54 4.6 24.0 1.0
CZ A:PHE91 4.7 24.7 1.0
HD11 A:LEU57 4.7 22.5 1.0
C A:LEU57 4.8 17.7 1.0
HG12 A:ILE99 4.8 20.1 1.0
CA A:LEU57 4.8 17.8 1.0
H6 A:G7I201 4.8 17.9 1.0
CE1 A:PHE91 4.9 24.4 1.0
HD12 A:ILE103 4.9 20.9 1.0
O A:LEU57 4.9 18.5 1.0
CE1 A:PHE86 5.0 25.0 1.0
HG13 A:ILE61 5.0 21.3 1.0

Chlorine binding site 2 out of 6 in 8pwc

Go back to Chlorine Binding Sites List in 8pwc
Chlorine binding site 2 out of 6 in the Crystal Structure of MDM2 with Brigimadlin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of MDM2 with Brigimadlin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:20.8
occ:1.00
 CL19 A:G7I201 0.0 20.8 1.0
C15 A:G7I201 1.7 18.2 1.0
C14 A:G7I201 2.7 18.2 1.0
C16 A:G7I201 2.7 16.4 1.0
H16 A:G7I201 2.9 16.4 1.0
F21 A:G7I201 2.9 19.8 1.0
HA A:HIS96 2.9 18.9 1.0
HE1 A:TYR100 2.9 19.5 1.0
HD13 A:LEU54 2.9 28.5 1.0
HB3 A:HIS96 2.9 19.0 1.0
HD22 A:LEU54 3.0 24.0 1.0
HD21 A:LEU54 3.0 24.0 1.0
HD1 A:TYR100 3.1 20.6 1.0
HB A:ILE99 3.2 20.0 1.0
CD2 A:LEU54 3.5 24.0 1.0
CG A:HIS96 3.5 18.9 1.0
CB A:HIS96 3.5 19.1 1.0
HG22 A:ILE99 3.5 20.8 1.0
HG21 A:ILE99 3.6 20.9 1.0
HD12 A:ILE99 3.7 21.4 1.0
CA A:HIS96 3.7 19.0 1.0
CE1 A:TYR100 3.7 19.5 1.0
CD1 A:TYR100 3.7 20.6 1.0
O A:HIS96 3.8 19.6 1.0
CD1 A:LEU54 3.8 28.5 1.0
HD11 A:LEU54 3.8 28.5 1.0
CD2 A:HIS96 3.8 19.5 1.0
CG2 A:ILE99 3.9 20.9 1.0
ND1 A:HIS96 3.9 21.0 1.0
C17 A:G7I201 4.0 16.9 1.0
CB A:ILE99 4.0 20.1 1.0
C13 A:G7I201 4.0 16.4 1.0
HD2 A:HIS96 4.1 19.5 1.0
HD13 A:ILE99 4.1 21.5 1.0
C A:HIS96 4.2 18.7 1.0
CG A:LEU54 4.2 23.5 1.0
CD1 A:ILE99 4.3 21.5 1.0
NE2 A:HIS96 4.4 21.0 1.0
HD23 A:LEU54 4.4 24.0 1.0
HG13 A:ILE19 4.4 23.6 1.0
CE1 A:HIS96 4.4 20.8 1.0
H A:TYR100 4.4 20.6 1.0
C18 A:G7I201 4.5 16.5 1.0
HB2 A:HIS96 4.5 19.0 1.0
O A:HOH329 4.6 25.6 1.0
HD12 A:LEU54 4.7 28.5 1.0
HB3 A:LEU54 4.7 18.5 1.0
CG1 A:ILE99 4.8 20.1 1.0
O A:HOH323 4.8 28.2 1.0
H17 A:G7I201 4.9 17.1 1.0
N A:HIS96 4.9 20.2 1.0
N A:TYR100 4.9 20.6 1.0
CZ A:TYR100 4.9 21.0 1.0
HG A:LEU54 4.9 23.4 1.0
HG23 A:ILE99 5.0 20.9 1.0
HE2 A:HIS96 5.0 21.1 1.0

Chlorine binding site 3 out of 6 in 8pwc

Go back to Chlorine Binding Sites List in 8pwc
Chlorine binding site 3 out of 6 in the Crystal Structure of MDM2 with Brigimadlin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of MDM2 with Brigimadlin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:21.9
occ:1.00
 CL12 B:G7I201 0.0 21.9 1.0
C4 B:G7I201 1.7 19.5 1.0
C3 B:G7I201 2.7 19.5 1.0
C5 B:G7I201 2.7 18.3 1.0
H3 B:G7I201 2.8 19.6 1.0
H5 B:G7I201 2.8 18.3 1.0
HB3 B:LEU57 2.9 19.2 1.0
HZ B:PHE86 3.0 23.2 1.0
HD11 B:ILE61 3.1 23.1 1.0
HD12 B:LEU57 3.2 23.5 1.0
HE2 B:PHE86 3.3 25.1 1.0
HG21 B:ILE99 3.3 22.0 1.0
HB2 B:LEU57 3.4 19.2 1.0
HD11 B:ILE103 3.4 23.2 1.0
HD23 B:LEU54 3.4 21.8 1.0
HD13 B:LEU57 3.5 23.5 1.0
HG23 B:ILE99 3.6 21.9 1.0
CB B:LEU57 3.6 19.2 1.0
CZ B:PHE86 3.8 23.1 1.0
CD1 B:LEU57 3.8 23.5 1.0
CG2 B:ILE99 3.9 22.0 1.0
CE2 B:PHE86 3.9 25.1 1.0
HZ B:PHE91 3.9 26.1 1.0
CD1 B:ILE61 3.9 23.1 1.0
HD12 B:ILE61 3.9 23.2 1.0
C8 B:G7I201 3.9 17.7 1.0
C6 B:G7I201 4.0 19.1 1.0
HD11 B:LEU82 4.0 31.2 1.0
HD21 B:LEU82 4.3 30.1 1.0
CD2 B:LEU54 4.3 21.8 1.0
HD22 B:LEU54 4.3 21.8 1.0
CG B:LEU57 4.3 22.1 1.0
HG22 B:ILE99 4.3 21.9 1.0
HD13 B:ILE99 4.4 22.7 1.0
HD13 B:ILE61 4.4 23.2 1.0
C7 B:G7I201 4.5 17.9 1.0
HD21 B:LEU54 4.5 21.9 1.0
HA B:LEU54 4.5 17.2 1.0
CZ B:PHE91 4.5 26.1 1.0
HE1 B:PHE91 4.5 27.1 1.0
CD1 B:ILE103 4.5 23.2 1.0
HD22 B:LEU57 4.7 24.6 1.0
HG12 B:ILE99 4.7 22.2 1.0
HD11 B:LEU57 4.8 23.5 1.0
C B:LEU57 4.8 19.3 1.0
CA B:LEU57 4.8 18.9 1.0
H6 B:G7I201 4.8 19.1 1.0
CE1 B:PHE91 4.9 27.1 1.0
HG13 B:ILE103 4.9 21.2 1.0
HG13 B:ILE61 5.0 23.4 1.0
CE1 B:PHE86 5.0 23.2 1.0
O B:LEU57 5.0 20.8 1.0

Chlorine binding site 4 out of 6 in 8pwc

Go back to Chlorine Binding Sites List in 8pwc
Chlorine binding site 4 out of 6 in the Crystal Structure of MDM2 with Brigimadlin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of MDM2 with Brigimadlin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:22.9
occ:1.00
 CL19 B:G7I201 0.0 22.9 1.0
C15 B:G7I201 1.7 20.5 1.0
C14 B:G7I201 2.7 20.5 1.0
C16 B:G7I201 2.7 19.6 1.0
H16 B:G7I201 2.9 19.6 1.0
F21 B:G7I201 2.9 21.1 1.0
HA B:HIS96 2.9 20.7 1.0
HE1 B:TYR100 2.9 21.9 1.0
HB3 B:HIS96 2.9 21.3 1.0
HD13 B:LEU54 3.0 26.3 1.0
HD22 B:LEU54 3.0 21.8 1.0
HB B:ILE99 3.1 21.2 1.0
HD1 B:TYR100 3.1 22.9 1.0
HD21 B:LEU54 3.2 21.9 1.0
CB B:HIS96 3.5 21.3 1.0
HD12 B:ILE99 3.5 22.7 1.0
CG B:HIS96 3.5 19.8 1.0
HG21 B:ILE99 3.5 22.0 1.0
CD2 B:LEU54 3.6 21.8 1.0
HG22 B:ILE99 3.6 21.9 1.0
CA B:HIS96 3.7 20.7 1.0
CE1 B:TYR100 3.7 21.9 1.0
O B:HIS96 3.8 22.4 1.0
CD1 B:TYR100 3.8 22.9 1.0
CD1 B:LEU54 3.8 26.3 1.0
HD11 B:LEU54 3.8 26.3 1.0
CD2 B:HIS96 3.9 19.8 1.0
ND1 B:HIS96 3.9 21.7 1.0
CG2 B:ILE99 3.9 22.0 1.0
CB B:ILE99 3.9 21.3 1.0
C17 B:G7I201 4.0 18.3 1.0
C13 B:G7I201 4.0 17.7 1.0
C B:HIS96 4.2 21.1 1.0
HD2 B:HIS96 4.2 19.8 1.0
CG B:LEU54 4.2 22.8 1.0
HD13 B:ILE99 4.3 22.7 1.0
CD1 B:ILE99 4.3 22.8 1.0
NE2 B:HIS96 4.4 19.9 1.0
HG13 B:ILE19 4.4 26.5 1.0
CE1 B:HIS96 4.4 20.9 1.0
H B:TYR100 4.5 21.3 1.0
C18 B:G7I201 4.5 17.4 1.0
HD23 B:LEU54 4.5 21.8 1.0
HB2 B:HIS96 4.5 21.3 1.0
O B:HOH342 4.6 27.1 1.0
CG1 B:ILE99 4.7 22.2 1.0
HB3 B:LEU54 4.7 18.4 1.0
HD12 B:LEU54 4.8 26.3 1.0
H17 B:G7I201 4.8 18.5 1.0
N B:HIS96 4.9 22.0 1.0
O B:HOH335 4.9 30.8 1.0
N B:TYR100 4.9 21.2 1.0
HH B:TYR100 4.9 25.1 1.0
HE2 B:HIS96 5.0 20.0 1.0
HG23 B:ILE99 5.0 21.9 1.0
CZ B:TYR100 5.0 22.5 1.0

Chlorine binding site 5 out of 6 in 8pwc

Go back to Chlorine Binding Sites List in 8pwc
Chlorine binding site 5 out of 6 in the Crystal Structure of MDM2 with Brigimadlin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of MDM2 with Brigimadlin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl201

b:43.7
occ:0.86
 CL12 C:G7I201 0.0 43.7 0.9
C4 C:G7I201 1.7 43.8 0.9
HD23 C:LEU57 2.6 59.7 1.0
C5 C:G7I201 2.7 43.7 0.9
C3 C:G7I201 2.7 44.1 0.9
HB3 C:LEU57 2.7 55.5 1.0
H3 C:G7I201 2.8 44.1 0.9
H5 C:G7I201 2.8 43.7 0.9
HZ C:PHE86 2.9 71.3 1.0
HG21 C:ILE99 3.1 55.9 1.0
HE2 C:PHE86 3.3 71.8 1.0
HD11 C:ILE61 3.3 58.1 1.0
HD23 C:LEU54 3.3 52.5 1.0
HD11 C:ILE103 3.4 56.6 1.0
HB2 C:LEU57 3.4 55.5 1.0
CB C:LEU57 3.5 55.5 1.0
HG23 C:ILE99 3.5 55.9 1.0
CD2 C:LEU57 3.6 59.7 1.0
CZ C:PHE86 3.7 71.2 1.0
CG2 C:ILE99 3.8 55.9 1.0
HD22 C:LEU57 3.8 59.7 1.0
HD12 C:ILE61 3.8 58.1 1.0
CE2 C:PHE86 3.9 71.8 1.0
CG C:LEU57 4.0 58.8 1.0
C8 C:G7I201 4.0 43.9 0.9
C6 C:G7I201 4.0 44.2 0.9
CD1 C:ILE61 4.0 58.1 1.0
HG C:LEU57 4.0 58.8 1.0
HZ C:PHE91 4.1 62.4 1.0
HD11 C:LEU82 4.1 71.4 1.0
HG22 C:ILE99 4.1 55.9 1.0
CD2 C:LEU54 4.2 52.5 1.0
HD22 C:LEU54 4.3 52.5 1.0
HA C:LEU54 4.4 48.7 1.0
HD13 C:ILE99 4.4 56.8 1.0
HD21 C:LEU57 4.4 59.7 1.0
CD1 C:ILE103 4.4 56.6 1.0
HD13 C:ILE61 4.4 58.1 1.0
C7 C:G7I201 4.5 44.2 0.9
HD21 C:LEU54 4.5 52.5 1.0
HD21 C:LEU82 4.6 71.2 1.0
HE1 C:PHE91 4.6 62.7 1.0
CZ C:PHE91 4.7 62.4 1.0
HG12 C:ILE99 4.7 56.0 1.0
HD13 C:ILE103 4.7 56.6 1.0
CA C:LEU57 4.8 54.2 1.0
C C:LEU57 4.8 54.8 1.0
H6 C:G7I201 4.8 44.2 0.9
HG13 C:ILE103 4.9 55.9 1.0
CE1 C:PHE91 4.9 62.7 1.0
CE1 C:PHE86 5.0 71.3 1.0
HG12 C:ILE103 5.0 55.9 1.0

Chlorine binding site 6 out of 6 in 8pwc

Go back to Chlorine Binding Sites List in 8pwc
Chlorine binding site 6 out of 6 in the Crystal Structure of MDM2 with Brigimadlin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of MDM2 with Brigimadlin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl201

b:46.1
occ:0.86
 CL19 C:G7I201 0.0 46.1 0.9
C15 C:G7I201 1.7 45.0 0.9
C14 C:G7I201 2.7 44.4 0.9
C16 C:G7I201 2.7 44.7 0.9
H16 C:G7I201 2.9 44.7 0.9
HD21 C:LEU54 2.9 52.5 1.0
F21 C:G7I201 2.9 43.6 0.9
HE1 C:TYR100 2.9 51.8 1.0
HD22 C:LEU54 2.9 52.5 1.0
HA C:HIS96 3.0 53.6 1.0
HB3 C:HIS96 3.0 52.2 1.0
HD13 C:LEU54 3.0 53.4 1.0
HD1 C:TYR100 3.1 50.7 1.0
HB C:ILE99 3.2 55.5 1.0
CD2 C:LEU54 3.4 52.5 1.0
CG C:HIS96 3.4 51.7 1.0
CB C:HIS96 3.5 52.2 1.0
HG22 C:ILE99 3.6 55.9 1.0
HD12 C:ILE99 3.6 56.8 1.0
HD11 C:LEU54 3.6 53.4 1.0
CA C:HIS96 3.7 53.6 1.0
CE1 C:TYR100 3.7 51.8 1.0
CD1 C:LEU54 3.7 53.4 1.0
O C:HIS96 3.7 53.9 1.0
CD1 C:TYR100 3.8 50.7 1.0
HG21 C:ILE99 3.8 55.9 1.0
ND1 C:HIS96 3.8 52.2 1.0
CD2 C:HIS96 3.8 52.2 1.0
CG2 C:ILE99 4.0 55.9 1.0
C17 C:G7I201 4.0 44.2 0.9
C13 C:G7I201 4.0 44.7 0.9
CB C:ILE99 4.0 55.5 1.0
CG C:LEU54 4.1 51.5 1.0
HD2 C:HIS96 4.2 52.2 1.0
C C:HIS96 4.2 54.0 1.0
HD23 C:LEU54 4.3 52.5 1.0
HG13 C:ILE19 4.4 59.6 1.0
CE1 C:HIS96 4.4 52.8 1.0
NE2 C:HIS96 4.4 52.8 1.0
CD1 C:ILE99 4.4 56.8 1.0
HD13 C:ILE99 4.4 56.8 1.0
H C:TYR100 4.4 53.1 1.0
C18 C:G7I201 4.5 44.5 0.9
HB2 C:HIS96 4.5 52.2 1.0
HB3 C:LEU54 4.7 49.3 1.0
HD12 C:LEU54 4.7 53.4 1.0
CG1 C:ILE99 4.8 56.0 1.0
H17 C:G7I201 4.9 44.2 0.9
N C:HIS96 4.9 54.8 1.0
N C:TYR100 4.9 53.1 1.0
HG C:LEU54 4.9 51.5 1.0
CZ C:TYR100 5.0 52.4 1.0

Reference:

A.Gollner, D.Rudolph, U.Weyer-Czernilofsky, R.Baumgartinger, P.Jung, H.Weinstabl, J.Ramharter, R.Grempler, J.Quant, J.Rinnenthal, A.Perez Pitarch, B.Golubovic, D.Gerlach, G.Bader, K.Wetzel, S.Otto, C.Mandl, G.Boehmelt, D.B.Mcconnell, N.Kraut, P.Sini. Discovery and Characterization of Brigimadlin, A Novel and Highly Potent MDM2-P53 Antagonist Suitable For Intermittent Dose Schedules. Mol.Cancer Ther. 2024.
ISSN: ESSN 1538-8514
PubMed: 39259562
DOI: 10.1158/1535-7163.MCT-23-0783
Page generated: Thu Oct 31 17:56:09 2024

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