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US 2003/0224368 A1Published application
Crystallizable compositions comprising a caspase-7
OwnerYunyi Weiinventor
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OwnerYunyi Weiinventor
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The present invention relates to a data storage medium encoded with the structural coordinates of crystallized molecules and molecular complexes which comprise the active site binding pockets of caspase-7. Such data storage material is capable of displaying such molecules and molecular complexes, or their structural homologues, as a graphical three-dimensional representation on a computer screen. This invention also related to methods of using the structure coordinates to solve the structure of similar or homologous proteins or protein complexes. In addition, this invention relates to methods of using the structure coordinates to screen and design compounds, including inhibitory compounds, that bind to caspase-7 or homologues thereof. This invention also relates to molecules or molecular complexes which comprise the active site binding pockets of caspase-7 or close structural homologues of the active site binding pockets. The present invention also relates to compositions and crystals of a caspase-7 in complex with a caspase inhibitor. This invention also relates to compounds and pharmaceutical compositions which are inhibitors of caspase-7.
A molecule or molecular complex comprising all or any part of a binding pocket defined by structure coordinates of caspase-7 amino acids 234, 235, 237, 276, 278, 281, and 284 according to FIG. 7, or a homologue of said molecule or molecular complex, wherein said homologue comprises a binding pocket that has a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å, and wherein said molecule or molecular complex has a S4 binding region that is more hydrophilic than the S4 binding region of caspase-3.
A crystallizable composition comprising a caspase-7 or homologue thereof complexed with Ac-Asp-Glu-Val-Asp-CHO.
A crystal comprising a caspase-7 or homologue thereof complexed with Ac-Asp-Glu-Val-Asp-CHO.
A machine-readable data storage medium, comprising a data storage material encoded with machine readable data, wherein said data is defined by the all or a portion of the structure coordinates of a molecule or molecular complex according to FIG. 7, or a homologue of said molecule or molecular complex, wherein said homologue comprises backbone atoms that have a root mean square deviation from the backbone atoms of the complex of not more than 1.5 Å, and wherein said molecule or molecular complex has a S4 binding region that is more hydrophilic than the S4 binding region of caspase-3.
A machine-readable data storage medium comprising a data storage material encoded with a first set of machine readable data which, when combined with a second set of machine readable data using a machine programmed with instructions for using said first set of data and said second set of data, can determine at least a portion of the structure coordinates corresponding to the second set of machine readable data, wherein:
A computer for producing a three-dimensional representation of:
The computer according to claim 23, wherein said homologue comprises a binding pocket that has a root mean square deviation from the backbone atoms of said amino acids of not more than 1.0 Å.
A computer for determining at least a portion of the structure coordinates corresponding to X-ray diffraction data obtained from a molecule or molecular complex, wherein said computer comprises:
A method of utilizing molecular replacement to obtain structural information about a molecule or a molecular complex of unknown structure by using the structure coordinates set forth in FIG. 7, comprising the steps of:
Dependencies are inferred from the claim text.