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Chlorine in PDB 4jvr: Co-Crystal Structure of MDM2 with Inhibitor (2'S,3R,4'S,5'R)-N-(2- Aminoethyl)-6-Chloro-4'-(3-Chloro-2-Fluorophenyl)-2'-(2,2- Dimethylpropyl)-2-Oxo-1,2-Dihydrospiro[Indole-3,3'-Pyrrolidine]-5'- Carboxamide

Protein crystallography data

The structure of Co-Crystal Structure of MDM2 with Inhibitor (2'S,3R,4'S,5'R)-N-(2- Aminoethyl)-6-Chloro-4'-(3-Chloro-2-Fluorophenyl)-2'-(2,2- Dimethylpropyl)-2-Oxo-1,2-Dihydrospiro[Indole-3,3'-Pyrrolidine]-5'- Carboxamide, PDB code: 4jvr was solved by X.Huang, F.Gonzalez-Lopez De Turiso, D.Sun, R.Yosup, M.D.Bartberger, H.P.Beck, J.Cannon, P.Shaffer, J.D.Oliner, S.H.Olson, J.C.Medina, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 56.678, 98.376, 104.574, 90.00, 90.00, 90.00
R / Rfree (%) 25.6 / 27

Other elements in 4jvr:

The structure of Co-Crystal Structure of MDM2 with Inhibitor (2'S,3R,4'S,5'R)-N-(2- Aminoethyl)-6-Chloro-4'-(3-Chloro-2-Fluorophenyl)-2'-(2,2- Dimethylpropyl)-2-Oxo-1,2-Dihydrospiro[Indole-3,3'-Pyrrolidine]-5'- Carboxamide also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Co-Crystal Structure of MDM2 with Inhibitor (2'S,3R,4'S,5'R)-N-(2- Aminoethyl)-6-Chloro-4'-(3-Chloro-2-Fluorophenyl)-2'-(2,2- Dimethylpropyl)-2-Oxo-1,2-Dihydrospiro[Indole-3,3'-Pyrrolidine]-5'- Carboxamide (pdb code 4jvr). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Co-Crystal Structure of MDM2 with Inhibitor (2'S,3R,4'S,5'R)-N-(2- Aminoethyl)-6-Chloro-4'-(3-Chloro-2-Fluorophenyl)-2'-(2,2- Dimethylpropyl)-2-Oxo-1,2-Dihydrospiro[Indole-3,3'-Pyrrolidine]-5'- Carboxamide, PDB code: 4jvr:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4jvr

Go back to Chlorine Binding Sites List in 4jvr
Chlorine binding site 1 out of 6 in the Co-Crystal Structure of MDM2 with Inhibitor (2'S,3R,4'S,5'R)-N-(2- Aminoethyl)-6-Chloro-4'-(3-Chloro-2-Fluorophenyl)-2'-(2,2- Dimethylpropyl)-2-Oxo-1,2-Dihydrospiro[Indole-3,3'-Pyrrolidine]-5'- Carboxamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Co-Crystal Structure of MDM2 with Inhibitor (2'S,3R,4'S,5'R)-N-(2- Aminoethyl)-6-Chloro-4'-(3-Chloro-2-Fluorophenyl)-2'-(2,2- Dimethylpropyl)-2-Oxo-1,2-Dihydrospiro[Indole-3,3'-Pyrrolidine]-5'- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:25.9
occ:1.00
 CL1 A:1MT201 0.0 25.9 1.0
C1 A:1MT201 1.7 25.9 1.0
C2 A:1MT201 2.7 26.1 1.0
C3 A:1MT201 2.8 25.6 1.0
F1 A:1MT201 2.9 25.8 1.0
CG A:HIS96 3.6 26.8 1.0
CE2 A:TYR100 3.6 23.9 1.0
O A:HIS96 3.8 24.8 1.0
CZ A:TYR100 3.8 22.9 1.0
CB A:HIS96 3.8 25.4 1.0
CG2 A:ILE99 3.8 20.7 1.0
ND1 A:HIS96 3.9 27.2 1.0
CD2 A:LEU54 3.9 20.0 1.0
CD2 A:HIS96 3.9 26.7 1.0
CD2 A:TYR100 3.9 23.0 1.0
CA A:HIS96 3.9 26.1 1.0
C6 A:1MT201 4.0 25.8 1.0
CB A:ILE99 4.1 19.8 1.0
C4 A:1MT201 4.1 26.4 1.0
CE1 A:TYR100 4.2 23.4 1.0
OH A:TYR100 4.2 25.5 1.0
CE1 A:HIS96 4.3 27.6 1.0
C A:HIS96 4.3 25.4 1.0
CG A:TYR100 4.3 21.1 1.0
NE2 A:HIS96 4.3 27.3 1.0
CD1 A:TYR100 4.4 22.2 1.0
C5 A:1MT201 4.5 25.6 1.0
CD1 A:ILE99 4.6 22.0 1.0
N A:TYR100 4.7 18.2 1.0
CD1 A:LEU54 4.8 21.9 1.0
CG1 A:ILE99 5.0 20.4 1.0

Chlorine binding site 2 out of 6 in 4jvr

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Chlorine binding site 2 out of 6 in the Co-Crystal Structure of MDM2 with Inhibitor (2'S,3R,4'S,5'R)-N-(2- Aminoethyl)-6-Chloro-4'-(3-Chloro-2-Fluorophenyl)-2'-(2,2- Dimethylpropyl)-2-Oxo-1,2-Dihydrospiro[Indole-3,3'-Pyrrolidine]-5'- Carboxamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Co-Crystal Structure of MDM2 with Inhibitor (2'S,3R,4'S,5'R)-N-(2- Aminoethyl)-6-Chloro-4'-(3-Chloro-2-Fluorophenyl)-2'-(2,2- Dimethylpropyl)-2-Oxo-1,2-Dihydrospiro[Indole-3,3'-Pyrrolidine]-5'- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:23.4
occ:1.00
 CL2 A:1MT201 0.0 23.4 1.0
C22 A:1MT201 1.7 21.3 1.0
C23 A:1MT201 2.6 22.4 1.0
C21 A:1MT201 2.7 21.8 1.0
CD1 A:LEU57 3.7 19.5 1.0
CZ A:PHE86 3.8 20.6 1.0
CE2 A:PHE86 3.8 22.6 1.0
C24 A:1MT201 3.9 21.7 1.0
CB A:LEU57 3.9 18.9 1.0
C20 A:1MT201 4.0 22.9 1.0
CD1 A:ILE61 4.0 21.5 1.0
CG2 A:ILE99 4.1 20.7 1.0
CZ A:PHE91 4.2 22.2 1.0
CD1 A:ILE103 4.2 20.8 1.0
CG A:LEU57 4.4 20.4 1.0
C19 A:1MT201 4.4 24.5 1.0
CG1 A:ILE103 4.8 18.9 1.0
CE1 A:PHE91 4.8 23.4 1.0
CD2 A:LEU57 4.9 20.1 1.0

Chlorine binding site 3 out of 6 in 4jvr

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Chlorine binding site 3 out of 6 in the Co-Crystal Structure of MDM2 with Inhibitor (2'S,3R,4'S,5'R)-N-(2- Aminoethyl)-6-Chloro-4'-(3-Chloro-2-Fluorophenyl)-2'-(2,2- Dimethylpropyl)-2-Oxo-1,2-Dihydrospiro[Indole-3,3'-Pyrrolidine]-5'- Carboxamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Co-Crystal Structure of MDM2 with Inhibitor (2'S,3R,4'S,5'R)-N-(2- Aminoethyl)-6-Chloro-4'-(3-Chloro-2-Fluorophenyl)-2'-(2,2- Dimethylpropyl)-2-Oxo-1,2-Dihydrospiro[Indole-3,3'-Pyrrolidine]-5'- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl201

b:25.7
occ:1.00
 CL1 C:1MT201 0.0 25.7 1.0
C1 C:1MT201 1.7 25.6 1.0
C3 C:1MT201 2.7 24.8 1.0
C2 C:1MT201 2.7 25.2 1.0
F1 C:1MT201 3.0 25.4 1.0
CE2 C:TYR100 3.4 23.4 1.0
CB C:HIS96 3.5 25.8 1.0
CG C:HIS96 3.6 28.2 1.0
O C:HIS96 3.6 26.1 1.0
CD2 C:TYR100 3.7 21.4 1.0
CA C:HIS96 3.7 26.8 1.0
CG2 C:ILE99 3.8 19.7 1.0
CZ C:TYR100 3.8 22.1 1.0
CB C:ILE99 3.9 20.2 1.0
ND1 C:HIS96 3.9 28.5 1.0
C4 C:1MT201 4.0 26.6 1.0
C6 C:1MT201 4.1 26.6 1.0
C C:HIS96 4.1 26.6 1.0
CD2 C:LEU54 4.1 20.7 1.0
CD2 C:HIS96 4.2 28.8 1.0
CG C:TYR100 4.3 20.1 1.0
OH C:TYR100 4.3 26.0 1.0
CD1 C:ILE99 4.4 22.0 1.0
CE1 C:TYR100 4.4 23.5 1.0
C5 C:1MT201 4.5 25.1 1.0
N C:TYR100 4.5 17.5 1.0
CE1 C:HIS96 4.6 29.1 1.0
CD1 C:TYR100 4.6 22.1 1.0
NE2 C:HIS96 4.7 29.5 1.0
CG1 C:ILE99 4.7 20.7 1.0
CD1 C:LEU54 4.9 20.5 1.0
CA C:ILE99 5.0 19.6 1.0
C C:ILE99 5.0 18.5 1.0
N C:HIS96 5.0 28.0 1.0

Chlorine binding site 4 out of 6 in 4jvr

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Chlorine binding site 4 out of 6 in the Co-Crystal Structure of MDM2 with Inhibitor (2'S,3R,4'S,5'R)-N-(2- Aminoethyl)-6-Chloro-4'-(3-Chloro-2-Fluorophenyl)-2'-(2,2- Dimethylpropyl)-2-Oxo-1,2-Dihydrospiro[Indole-3,3'-Pyrrolidine]-5'- Carboxamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Co-Crystal Structure of MDM2 with Inhibitor (2'S,3R,4'S,5'R)-N-(2- Aminoethyl)-6-Chloro-4'-(3-Chloro-2-Fluorophenyl)-2'-(2,2- Dimethylpropyl)-2-Oxo-1,2-Dihydrospiro[Indole-3,3'-Pyrrolidine]-5'- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl201

b:23.6
occ:1.00
 CL2 C:1MT201 0.0 23.6 1.0
C22 C:1MT201 1.6 21.6 1.0
C23 C:1MT201 2.6 22.2 1.0
C21 C:1MT201 2.7 21.9 1.0
CD1 C:LEU57 3.7 19.9 1.0
CZ C:PHE86 3.7 21.1 1.0
CE2 C:PHE86 3.7 21.6 1.0
CD1 C:ILE61 3.8 24.1 1.0
C24 C:1MT201 3.8 22.8 1.0
CB C:LEU57 3.9 19.6 1.0
C20 C:1MT201 4.0 22.8 1.0
CG2 C:ILE99 4.2 19.7 1.0
CG C:LEU57 4.3 19.8 1.0
CZ C:PHE91 4.3 24.2 1.0
CD1 C:ILE103 4.4 19.3 1.0
C19 C:1MT201 4.4 24.1 1.0
CD2 C:LEU57 4.7 20.8 1.0
CG1 C:ILE103 4.8 18.3 1.0
CE1 C:PHE91 4.9 25.4 1.0
CG1 C:ILE61 4.9 28.9 1.0
CE1 C:PHE86 5.0 21.1 1.0
N2 C:1MT201 5.0 24.4 1.0

Chlorine binding site 5 out of 6 in 4jvr

Go back to Chlorine Binding Sites List in 4jvr
Chlorine binding site 5 out of 6 in the Co-Crystal Structure of MDM2 with Inhibitor (2'S,3R,4'S,5'R)-N-(2- Aminoethyl)-6-Chloro-4'-(3-Chloro-2-Fluorophenyl)-2'-(2,2- Dimethylpropyl)-2-Oxo-1,2-Dihydrospiro[Indole-3,3'-Pyrrolidine]-5'- Carboxamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Co-Crystal Structure of MDM2 with Inhibitor (2'S,3R,4'S,5'R)-N-(2- Aminoethyl)-6-Chloro-4'-(3-Chloro-2-Fluorophenyl)-2'-(2,2- Dimethylpropyl)-2-Oxo-1,2-Dihydrospiro[Indole-3,3'-Pyrrolidine]-5'- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl201

b:25.6
occ:1.00
 CL1 E:1MT201 0.0 25.6 1.0
C1 E:1MT201 1.7 26.1 1.0
C2 E:1MT201 2.7 25.7 1.0
C3 E:1MT201 2.8 25.0 1.0
F1 E:1MT201 2.9 27.4 1.0
CG E:HIS96 3.4 27.2 1.0
CB E:HIS96 3.5 25.1 1.0
CE2 E:TYR100 3.5 21.7 1.0
CG2 E:ILE99 3.6 21.6 1.0
O E:HIS96 3.7 24.5 1.0
CA E:HIS96 3.7 26.4 1.0
CD2 E:TYR100 3.8 20.4 1.0
CD2 E:HIS96 3.8 27.6 1.0
CZ E:TYR100 3.8 20.7 1.0
ND1 E:HIS96 3.9 27.7 1.0
CB E:ILE99 3.9 21.0 1.0
CD2 E:LEU54 4.0 20.1 1.0
C6 E:1MT201 4.1 27.2 1.0
C4 E:1MT201 4.1 27.8 1.0
C E:HIS96 4.1 25.5 1.0
OH E:TYR100 4.3 24.0 1.0
CG E:TYR100 4.3 18.9 1.0
CE1 E:TYR100 4.4 21.6 1.0
NE2 E:HIS96 4.4 27.8 1.0
CE1 E:HIS96 4.4 28.1 1.0
C5 E:1MT201 4.5 25.8 1.0
CD1 E:ILE99 4.6 23.0 1.0
CD1 E:TYR100 4.6 21.5 1.0
N E:TYR100 4.6 18.3 1.0
CG1 E:ILE99 4.9 21.5 1.0
O E:HOH316 4.9 42.7 1.0
N E:HIS96 5.0 27.7 1.0

Chlorine binding site 6 out of 6 in 4jvr

Go back to Chlorine Binding Sites List in 4jvr
Chlorine binding site 6 out of 6 in the Co-Crystal Structure of MDM2 with Inhibitor (2'S,3R,4'S,5'R)-N-(2- Aminoethyl)-6-Chloro-4'-(3-Chloro-2-Fluorophenyl)-2'-(2,2- Dimethylpropyl)-2-Oxo-1,2-Dihydrospiro[Indole-3,3'-Pyrrolidine]-5'- Carboxamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Co-Crystal Structure of MDM2 with Inhibitor (2'S,3R,4'S,5'R)-N-(2- Aminoethyl)-6-Chloro-4'-(3-Chloro-2-Fluorophenyl)-2'-(2,2- Dimethylpropyl)-2-Oxo-1,2-Dihydrospiro[Indole-3,3'-Pyrrolidine]-5'- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl201

b:23.7
occ:1.00
 CL2 E:1MT201 0.0 23.7 1.0
C22 E:1MT201 1.7 21.5 1.0
C23 E:1MT201 2.6 22.5 1.0
C21 E:1MT201 2.7 21.3 1.0
CZ E:PHE86 3.7 20.4 1.0
CE2 E:PHE86 3.7 21.0 1.0
CD1 E:LEU57 3.9 18.9 1.0
C24 E:1MT201 3.9 22.1 1.0
C20 E:1MT201 4.0 22.1 1.0
CD1 E:ILE61 4.0 23.6 1.0
CB E:LEU57 4.0 18.2 1.0
CZ E:PHE91 4.3 24.9 1.0
CG2 E:ILE99 4.3 21.6 1.0
CD1 E:ILE103 4.4 19.7 1.0
C19 E:1MT201 4.4 23.9 1.0
CG E:LEU57 4.5 18.8 1.0
CG1 E:ILE103 4.8 19.3 1.0
CE1 E:PHE91 4.8 26.2 1.0
CD1 E:LEU82 4.9 31.1 1.0
CD2 E:LEU57 4.9 20.3 1.0
CE1 E:PHE86 4.9 20.0 1.0

Reference:

F.Gonzalez-Lopez De Turiso, D.Sun, Y.Rew, M.D.Bartberger, H.P.Beck, J.Canon, A.Chen, D.Chow, T.L.Correll, X.Huang, L.D.Julian, F.Kayser, M.C.Lo, A.M.Long, D.Mcminn, J.D.Oliner, T.Osgood, J.P.Powers, A.Y.Saiki, S.Schneider, P.Shaffer, S.H.Xiao, P.Yakowec, X.Yan, Q.Ye, D.Yu, X.Zhao, J.Zhou, J.C.Medina, S.H.Olson. Rational Design and Binding Mode Duality of MDM2-P53 Inhibitors. J.Med.Chem. V. 56 4053 2013.
ISSN: ISSN 0022-2623
PubMed: 23597064
DOI: 10.1021/JM400293Z
Page generated: Sun Jul 21 17:46:01 2024

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