Bromine 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 / R_free (%)*	20.7 / 28.2

Other elements in 4oc6:

Chlorine

(Cl)

2 atoms

Bromine Binding Sites:

The binding sites of Bromine 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 Bromine atom.
In total only one binding site of Bromine was 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:

Bromine binding site 1 out of 1 in 4oc6

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Bromine Binding Sites List in 4oc6

Bromine binding site 1 out of 1 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 Bromine with other atoms in the Br 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:Br402 b:0.4 occ:1.00	BR	B:2S1402	0.0	0.4	1.0
	C5	B:2S1402	1.9	0.2	1.0
	C6	B:2S1402	2.8	96.4	1.0
	C3	B:2S1402	2.9	90.5	1.0
	O4	B:2S1402	3.3	80.9	1.0
	C2	B:2S1402	3.3	80.3	1.0
	CL2	B:2S1402	3.4	90.6	1.0
	O1	B:GOL403	3.5	0.2	1.0
	CA	A:GLY79	4.0	82.6	1.0
	C7	B:2S1402	4.1	89.8	1.0
	C	A:GLY79	4.2	86.8	1.0
	C9	B:2S1402	4.2	86.9	1.0
	N	A:SER80	4.3	82.0	1.0
	N1	B:2S1402	4.3	71.7	1.0
	OG1	B:THR234	4.4	71.5	1.0
	C1	B:GOL403	4.4	0.8	1.0
	SD	B:MET309	4.5	96.7	1.0
	C8	B:2S1402	4.7	85.7	1.0
	C30	B:2S1402	4.7	71.3	1.0
	O	A:GLY79	4.8	88.2	1.0
	CB	A:SER80	4.8	82.8	1.0
	OG	A:SER80	4.9	89.7	1.0
	N	A:GLY79	4.9	80.3	1.0
	CG2	B:THR234	5.0	56.8	1.0
	CA	A:SER80	5.0	82.3	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: Mon Jul 7 07:12:01 2025

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