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Chlorine in PDB 4oc6: Structure of Cathepsin D with Inhibitor 2-Bromo-N-[(2S,3S)-4-{[2-(2,4- Dichlorophenyl)Ethyl][3-(1,3-Dioxo-1,3-Dihydro-2H-Isoindol-2-Yl) Propanoyl]Amino}-3-Hydroxy-1-(3-Phenoxyphenyl)Butan-2-Yl]-4,5- Dimethoxybenzamide

Enzymatic activity of Structure of Cathepsin D with Inhibitor 2-Bromo-N-[(2S,3S)-4-{[2-(2,4- Dichlorophenyl)Ethyl][3-(1,3-Dioxo-1,3-Dihydro-2H-Isoindol-2-Yl) Propanoyl]Amino}-3-Hydroxy-1-(3-Phenoxyphenyl)Butan-2-Yl]-4,5- Dimethoxybenzamide

All present enzymatic activity of Structure of Cathepsin D with Inhibitor 2-Bromo-N-[(2S,3S)-4-{[2-(2,4- Dichlorophenyl)Ethyl][3-(1,3-Dioxo-1,3-Dihydro-2H-Isoindol-2-Yl) Propanoyl]Amino}-3-Hydroxy-1-(3-Phenoxyphenyl)Butan-2-Yl]-4,5- Dimethoxybenzamide:
3.4.23.5;

Protein crystallography data

The structure of Structure of Cathepsin D with Inhibitor 2-Bromo-N-[(2S,3S)-4-{[2-(2,4- Dichlorophenyl)Ethyl][3-(1,3-Dioxo-1,3-Dihydro-2H-Isoindol-2-Yl) Propanoyl]Amino}-3-Hydroxy-1-(3-Phenoxyphenyl)Butan-2-Yl]-4,5- Dimethoxybenzamide, PDB code: 4oc6 was solved by U.Graedler, P.Czodrowski, C.Tsaklakidis, M.Klein, K.Maskos, B.Leuthner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.76 / 2.64
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 77.022, 77.022, 251.586, 90.00, 90.00, 120.00
R / Rfree (%) 20.7 / 28.2

Other elements in 4oc6:

The structure of Structure of Cathepsin D with Inhibitor 2-Bromo-N-[(2S,3S)-4-{[2-(2,4- Dichlorophenyl)Ethyl][3-(1,3-Dioxo-1,3-Dihydro-2H-Isoindol-2-Yl) Propanoyl]Amino}-3-Hydroxy-1-(3-Phenoxyphenyl)Butan-2-Yl]-4,5- Dimethoxybenzamide also contains other interesting chemical elements:

Bromine (Br) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Cathepsin D with Inhibitor 2-Bromo-N-[(2S,3S)-4-{[2-(2,4- Dichlorophenyl)Ethyl][3-(1,3-Dioxo-1,3-Dihydro-2H-Isoindol-2-Yl) Propanoyl]Amino}-3-Hydroxy-1-(3-Phenoxyphenyl)Butan-2-Yl]-4,5- Dimethoxybenzamide (pdb code 4oc6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Structure of Cathepsin D with Inhibitor 2-Bromo-N-[(2S,3S)-4-{[2-(2,4- Dichlorophenyl)Ethyl][3-(1,3-Dioxo-1,3-Dihydro-2H-Isoindol-2-Yl) Propanoyl]Amino}-3-Hydroxy-1-(3-Phenoxyphenyl)Butan-2-Yl]-4,5- Dimethoxybenzamide, PDB code: 4oc6:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4oc6

Go back to Chlorine Binding Sites List in 4oc6
Chlorine binding site 1 out of 2 in the Structure of Cathepsin D with Inhibitor 2-Bromo-N-[(2S,3S)-4-{[2-(2,4- Dichlorophenyl)Ethyl][3-(1,3-Dioxo-1,3-Dihydro-2H-Isoindol-2-Yl) Propanoyl]Amino}-3-Hydroxy-1-(3-Phenoxyphenyl)Butan-2-Yl]-4,5- Dimethoxybenzamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Cathepsin D with Inhibitor 2-Bromo-N-[(2S,3S)-4-{[2-(2,4- Dichlorophenyl)Ethyl][3-(1,3-Dioxo-1,3-Dihydro-2H-Isoindol-2-Yl) Propanoyl]Amino}-3-Hydroxy-1-(3-Phenoxyphenyl)Butan-2-Yl]-4,5- Dimethoxybenzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:90.6
occ:1.00
 CL2 B:2S1402 0.0 90.6 1.0
C37 B:2S1402 1.7 84.8 1.0
C38 B:2S1402 2.6 86.0 1.0
C36 B:2S1402 2.8 78.8 1.0
C35 B:2S1402 3.1 74.8 1.0
BR B:2S1402 3.4 0.4 1.0
C30 B:2S1402 3.5 71.3 1.0
N33 B:2S1402 3.5 71.5 1.0
CA A:GLY79 3.7 82.6 1.0
C44 B:2S1402 3.9 75.1 1.0
C39 B:2S1402 3.9 87.7 1.0
C34 B:2S1402 3.9 71.3 1.0
CD1 B:ILE320 4.0 73.8 1.0
C41 B:2S1402 4.0 79.4 1.0
O45 B:2S1402 4.1 71.8 1.0
N A:GLY79 4.2 80.3 1.0
C40 B:2S1402 4.5 82.7 1.0
C46 B:2S1402 4.7 80.4 1.0
O4 B:2S1402 4.8 80.9 1.0
SD B:MET309 4.8 96.7 1.0
C2 B:2S1402 4.9 80.3 1.0
C5 B:2S1402 4.9 0.2 1.0
C A:GLY79 4.9 86.8 1.0
C22 B:2S1402 5.0 65.9 1.0
OG1 B:THR234 5.0 71.5 1.0

Chlorine binding site 2 out of 2 in 4oc6

Go back to Chlorine Binding Sites List in 4oc6
Chlorine binding site 2 out of 2 in the Structure of Cathepsin D with Inhibitor 2-Bromo-N-[(2S,3S)-4-{[2-(2,4- Dichlorophenyl)Ethyl][3-(1,3-Dioxo-1,3-Dihydro-2H-Isoindol-2-Yl) Propanoyl]Amino}-3-Hydroxy-1-(3-Phenoxyphenyl)Butan-2-Yl]-4,5- Dimethoxybenzamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Cathepsin D with Inhibitor 2-Bromo-N-[(2S,3S)-4-{[2-(2,4- Dichlorophenyl)Ethyl][3-(1,3-Dioxo-1,3-Dihydro-2H-Isoindol-2-Yl) Propanoyl]Amino}-3-Hydroxy-1-(3-Phenoxyphenyl)Butan-2-Yl]-4,5- Dimethoxybenzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:97.0
occ:1.00
 CL1 B:2S1402 0.0 97.0 1.0
C39 B:2S1402 1.7 87.7 1.0
C38 B:2S1402 2.6 86.0 1.0
C40 B:2S1402 2.7 82.7 1.0
O58 B:2S1402 3.7 84.8 1.0
CG2 B:ILE311 3.8 83.7 1.0
C37 B:2S1402 3.9 84.8 1.0
C41 B:2S1402 4.0 79.4 1.0
CD B:PRO312 4.1 88.2 1.0
C36 B:2S1402 4.5 78.8 1.0
CB B:SER315 4.5 84.3 1.0
CG1 B:ILE311 4.7 79.7 1.0
CB B:ILE311 4.7 83.2 1.0
C49 B:2S1402 4.8 86.8 1.0
OG B:SER315 4.8 87.0 1.0
CA B:ILE311 4.9 82.9 1.0
CG B:PRO312 5.0 95.3 1.0
N B:PRO312 5.0 88.0 1.0

Reference:

U.Gradler, P.Czodrowski, C.Tsaklakidis, M.Klein, D.Werkmann, S.Lindemann, K.Maskos, B.Leuthner. Structure-Based Optimization of Non-Peptidic Cathepsin D Inhibitors. Bioorg.Med.Chem.Lett. V. 24 4141 2014.
ISSN: ISSN 0960-894X
PubMed: 25086681
DOI: 10.1016/J.BMCL.2014.07.054
Page generated: Thu Jul 25 23:22:49 2024

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