Claims
- 1. A method of producing a computer readable database comprising the three-dimensional molecular structural coordinates of binding pocket of a ATP-PRT protein, said method comprising
a) obtaining three-dimensional structural coordinates defining said protein or a binding pocket of said protein, from a crystal of said protein; and b) introducing said structural coordinates into a computer to produce a database containing the molecular structural coordinates of said protein or said binding pocket.
- 2. The method of claim 1 wherein said binding pocket comprises amino acids Lys, Arg, Glu, and Asp.
- 3. The method of claim 2 wherein said computer is capable of utilizing or displaying a three-dimensional molecular structure comprising said binding pocket using said structural coordinates.
- 4. The method of claim 2 wherein said binding pocket further comprises amino acids corresponding to Asp and Glu.
- 5. The method of claim 1 wherein said binding pocket comprises a binding pocket defined by the structural coordinates of at least three amino acids selected from the group consisting of Lys9, Arg46, Glu135, Asp148, Asp49, and Glu71.
- 6. The method of claim 5 wherein said binding pocket comprises Lys9, Arg46, Glu135, and Asp148 according to the sequence of FIG. 4 or 5.
- 7. The method of claim 6, wherein said binding pocket further comprises Asp49 and Glu71 according to the sequence of FIG. 4 or 5.
- 8. The method of claim 1, wherein said binding pocket comprises an active site.
- 9. A computer readable database produced by claim 1.
- 10. A method comprising electronic transmission of all or part of the computer readable database produced by claim 1.
- 11. A method of producing a computer readable database comprising a representation of a compound capable of binding a binding pocket of a ATP-PRT protein, said method comprising
a) introducing into a computer program a computer readable database produced by claim 1;b) generating a three-dimensional representation of a binding pocket of said ATP-PRT protein in said computer program; c) superimposing a three-dimensional model of at least one binding test compound on said representation of the binding pocket; d) assessing whether said test compound model fits spatially into the binding pocket of said ATP-PRT protein; and e) storing a representation of a compound that fits into the binding pocket into a computer readable database.
- 12. The method of claim 11 wherein in e), said representation is stored in the database produced by claim 1.
- 13. The method of claim 11, wherein said representation is selected from the group consisting of the compound's name, a chemical or molecular formula of the compound, a chemical structure of the compound, an identifier for the compound, and three-dimensional molecular structural coordinates of the compound.
- 14. The method of claim 11, wherein said generating of a three-dimensional representation of the binding pocket comprises use of structural coordinates having a root mean square deviation of the backbone atoms of the amino acid residues of said binding pocket of less than 2.0 Å from the structural coordinates of the corresponding residues according to FIG. 4 or 5.
- 15. The method of claim 11, wherein said at least one binding test compound is selected by a method selected from i) selecting a compound from a small molecule database, (ii) modifying a known inhibitor, substrate, reaction intermediate, or reaction product, or a portion thereof, of ATP-PRT, (iii) assembling chemical fragments or groups into a compound, and (iv) de novo ligand design of said compound.
- 16. The method of claim 11, wherein said assessing of whether a test compound model fits is by docking the model to said representation of said ATP-PRT binding pocket and/or performing energy minimization.
- 17. The method of claim 11 further comprising
f) preparing a binding test compound represented in said computer readable database; g) contacting said compound in a binding assay with a protein comprising said ATP-PRT protein binding pocket; h) determining whether said test compound binds to said protein in said assay; and i) introducing a representation of a compound that binds to said protein in said assay into a computer readable database.
- 18. The method of claim 17 wherein in i), said representation is stored in the database produced by claim 11.
- 19. The method of claim 17, wherein said representation is selected from the group consisting of the compound's name, a chemical formula of the compound, a chemical structure of the compound, an identifier for the compound, and three-dimensional molecular structural coordinates of the compound.
- 20. A method of producing a computer readable database comprising a representation of a binding pocket of a ATP-PRT protein in a co-crystal with a compound, said method comprising
a) preparing a binding test compound represented in a computer readable database produced by claim 11;b) forming a co-crystal of said compound with a protein comprising a binding pocket of a ATP-PRT protein; c) obtaining the structural coordinates of said binding pocket in said co-crystal; and d) introducing the structural coordinates of said binding pocket or said co-crystal into a computer-readable database.
- 21. The method of claim 20, further comprising introducing the structural coordinates of said compound in said co-crystal into said database.
- 22. The method of claim 11 wherein said binding pocket comprises amino acids Lys, Arg, Glu, and Asp.
- 23. The method of claim 22 wherein said computer is capable of utilizing or displaying a three-dimensional molecular structure of said binding pocket using said structural coordinates.
- 24. The method of claim 22 wherein said binding pocket further comprises amino acids corresponding to Asp and Glu.
- 25. The method of claim II wherein said binding pocket comprises a binding pocket defined by the structural coordinates of at least three amino acids selected from the group consisting of Lys9, Arg46, Glu135, Asp148, Asp49, and Glu71.
- 26. The method of claim 25 wherein said binding pocket comprises Lys9, Arg46, Glu135, and Asp148 according to the sequence of FIG. 4 or 5.
- 27. The method of claim 26, wherein said binding pocket further comprises Asp49 and Glu71 according to the sequence of FIG. 4 or 5.
- 28. The method of claim 11, wherein said binding pocket comprises an active site.
- 29. A computer readable database produced by claim 11.
- 30. A method comprising electronic transmission of all or part of the computer readable database produced by claim 11.
- 31. A method of modulating ATP-PRT protein activity comprising contacting said ATP-PRT with a compound, wherein said compound is represented in a database produced by the method of claim 11.
- 32. A method of producing a compound comprising a three-dimensional molecular structure represented by the coordinates contained in a computer readable database produced by claim 11 comprising synthesizing said compound wherein said compound fits a binding pocket of ATP-PRT protein.
- 33. A method of modulating ATP-PRT protein activity, comprising contacting said ATP-PRT protein with a compound produced by claim 32.
- 34. A method of identifying an activator or inhibitor of a protein that comprises a ATP-PRT active site or binding pocket, comprising
a) producing a compound according to claim 32;b) contacting said compound with a protein that comprises a ATP-PRT active site or binding pocket; and c) determining whether the potential modulator activates or inhibits the activity of said protein.
- 35. A method of producing an activator or inhibitor identified by claim 34.
- 36. A method of producing a computer readable database comprising a representation of a compound rationally designed to be capable of binding a binding pocket of a ATP-PRT protein, said method comprising
a) introducing into a computer program a computer readable database produced by claim 1;b) generating a three-dimensional representation of the protein or a binding pocket of said ATP-PRT protein in said computer program; c) designing a three-dimensional model of a compound that forms non-covalent bonds with amino acids of a binding pocket of said representation; and d) storing a representation of said compound into a computer readable database.
- 37. The method of claim 36, wherein said representation is selected from the group consisting of the compound's name, a chemical or molecular formula of the compound, a chemical structure of the compound, an identifier for the compound, and three-dimensional structural coordinates of the compound.
- 38. The method of claim 36 further comprising
e) preparing a binding test compound comprising a three-dimensional molecular structure represented by the coordinates contained in said computer readable database; f) contacting said compound in a binding assay with a protein comprising said binding pocket of a ATP-PRT protein; g) determining whether said test compound binds to said protein in said assay; and h) introducing a representation of a compound that binds to said protein in said assay into a computer-readable database.
- 39. The method of claim 38, wherein said representation is selected from the group consisting of the compound's name, a chemical or molecular formula of the compound, a chemical structure of the compound, an identifier for the compound, and three-dimensional structural coordinates of the compound.
- 40. A method of producing a computer readable database comprising a representation of a binding pocket of a ATP-PRT protein in a co-crystal with a compound rationally designed to be capable of binding said binding pocket, said method comprising
a) preparing a binding test compound represented in a computer readable database produced by claim 36;b) forming a co-crystal of said compound with a protein comprising a binding pocket of a ATP-PRT protein; c) obtaining the structural coordinates of said binding pocket in said co-crystal; and d) introducing the structural coordinates of said binding pocket or said co-crystal into a computer-readable database.
- 41. The method of claim 40, further comprising introducing the structural coordinates of said compound in said co-crystal into said database.
- 42. The method of claim 36 wherein said binding pocket comprises amino acids Lys, Arg, Glu, and Asp.
- 43. The method of claim 42 wherein said binding pocket further comprises amino acids corresponding to Asp and Glu.
- 44. The method of claim 36 wherein said binding pocket comprises a binding pocket defined by the structural coordinates of at least three amino acids selected from the group consisting of Lys9, Arg46, Glu135, Asp148, Asp49, and Glu71.
- 45. The method of claim 44 wherein said binding pocket comprises Lys9, Arg46, Glu135, and Asp148 according to the sequence of FIG. 4 or 5.
- 46. The method of claim 45, wherein said binding pocket further comprises Asp49 and Glu71 according to the sequence of FIG. 4 or 5.
- 47. The method of claim 36, wherein said binding pocket comprises an active site.
- 48. A computer readable database produced by claim 36.
- 49. A method comprising electronic transmission of all or part of the computer readable database produced by claim 36.
- 50. A method of producing a computer readable database comprising structural information about a molecule or a molecular complex of unknown structure comprising:
a) generating an x-ray diffraction pattern from a crystallized form of said molecule or molecular complex; b) using a molecular replacement method to interpret the structure of said molecule; wherein said molecular replacement method uses the structural coordinates of FIG. 4 or 5, or a subset thereof comprising a binding pocket, the structural coordinates of a binding pocket of FIG. 4 or 5, or structural coordinates having a root mean square deviation for the alpha-carbon atoms of said structural coordinates of less than 2.0 Å; and c) storing the coordinates of the resulting structure in a computer readable database.
- 51. The method of claim 50 wherein said binding pocket comprises a binding pocket defined by the structural coordinates of at least three amino acids selected from the group consisting of Lys9, Arg46, Glu135, Asp148, Asp49, and Glu71.
- 52. The method of claim 51 wherein said binding pocket comprises Lys9, Arg46, Glu135, and Asp148 according to the sequence of FIG. 4 or 5.
- 53. The method of claim 52, wherein said binding pocket further comprises Asp49 and Glu71 according to the sequence of FIG. 4 or 5.
- 54. The method of claim 50, wherein said binding pocket comprises an active site.
- 55. A computer readable database produced by claim 50.
- 56. A method comprising electronic transmission of all or part of the computer readable database produced by claim 50.
- 57. A method for homology modeling the structure of a ATP-PRT protein homolog comprising:
a) aligning the amino acid sequence of a ATP-PRT protein homolog with an amino acid sequence of ATP-PRT protein; b) incorporating the sequence of the ATP-PRT protein homolog into a model of the structure of ATP-PRT protein, wherein said model has the same structural coordinates as the structural coordinates of FIG. 4 or 5, or wherein the structural coordinates of said model's alpha-carbon atoms have a root mean square deviation from the structural coordinates of FIG. 4 or 5, of less than 2.0 Å to yield a preliminary model of said homolog; c) subjecting the preliminary model to energy minimization to yield an energy minimized model; and d) remodeling regions of the energy minimized model where stereochemistry restraints are violated to yield a final model of said homolog.
- 58. A method for identifying a compound that binds ATP-PRT protein comprising:
a) providing a computer modeling program with a set of structural coordinates or a three dimensional conformation for a molecule that comprises a binding pocket of ATP-PRT protein, or a homolog thereof; b) providing a said computer modeling program with a set of structural coordinates of a chemical entity; c) using said computer modeling program to evaluate the potential binding or interfering interactions between the chemical entity and said binding pocket; and d) determining whether said chemical entity potentially binds to or interferes with said protein or homolog.
- 59. The method of claim 58 further comprising the steps of:
e) computationally modifying the structural coordinates or three dimensional conformation of said chemical entity to improve the likelihood of binding to said binding pocket; and f) determining whether said modified chemical entity potentially binds to or interferes with said protein or homolog.
- 60. The method of claim 58 wherein determining whether the chemical entity potentially binds to said molecule comprises performing a fitting operation between the chemical entity and a binding pocket of the protein or homolog; and computationally analyzing the results of the fitting operation to quantify the association between, or the interference with, the chemical entity and the binding pocket.
- 61. The method of claim 58 wherein a library of structural coordinates of chemical entities is used to identify a compound that binds.
- 62. A method for designing a compound that binds ATP-PRT protein comprising:
a) providing a computer modeling program with a set of structural coordinates, or a three dimensional conformation derived therefrom, for a molecule that comprises a binding pocket comprising the structural coordinates of a binding pocket of ATP-PRT protein, or a homolog thereof; b) computationally building a chemical entity represented by set of structural coordinates; and c) determining whether the chemical entity is expected to bind to said molecule.
- 63. The method of claim 62, wherein determining whether the chemical entity potentially binds to said molecule comprises performing a fitting operation between the chemical entity and a binding pocket of the molecule; and
computationally analyzing the results of the fitting operation to quantify the association between the chemical entity and the binding pocket.
- 64. The method of claim 62 wherein said binding pocket comprises a binding pocket defined by the structural coordinates of at least three amino acids selected from the group consisting of Lys9, Arg46, Glu135, Asp148, Asp49, and Glu71.
- 65. The method of claim 64 wherein said binding pocket comprises Lys9, Arg46, Glu135, and Asp148 according to the sequence of FIG. 4 or 5.
- 66. The method of claim 65, wherein said binding pocket further comprises Asp49 and Glu71 according to the sequence of FIG. 4 or 5.
- 67. The method of claim 62, wherein said binding pocket comprises an active site.
- 68. A ATP-PRT protein, or a functional ATP-PRT protein subunit, in crystalline form.
- 69. The crystalline protein of claim 68, which is a heavy-atom derivative crystal.
- 70. The crystalline protein of claim 69, in which ATP-PRT protein is a mutant.
- 71. The crystalline protein of claim 70, which is characterized by a set of structural coordinates that is substantially similar to the set of structural coordinates of FIG. 4 or 5.
- 72. A machine-readable medium embedded with information that corresponds to a three-dimensional structural representation of a crystal of claim 68.
- 73. A machine-readable medium embedded with the molecular structural coordinates of FIG. 4 or 5, or at least 50% of the coordinates thereof.
- 74. A machine-readable medium embedded with the molecular structural coordinates of FIG. 4 or 5, or at least 80% of the coordinates thereof.
- 75. A machine-readable medium embedded with the molecular structural coordinates of a protein molecule comprising a ATP-PRT protein binding pocket, wherein said binding pocket comprises at least three amino acids selected from the group consisting of Lys9, Arg46, Glu135, Asp148, Asp49, and Glu71, having the structural coordinates of FIG. 4 or 5, or by the structural coordinates of a binding pocket homolog, wherein said the root mean square deviation of the backbone atoms of the amino acid residues of said binding pocket and said binding pocket homolog is less than 2.0 Å.
- 76. The machine-readable medium of claim 75, wherein said binding pocket comprises Lys9, Arg46, Glu135, and Asp148 according to the sequence of FIG. 4 or 5.
- 77. The machine-readable medium of claim 76, wherein said binding pocket further comprises Asp49 and Glu71 according to the sequence of FIG. 4 or 5.
- 78. A method of electronically transmitting all or part of the information stored in the machine-readable medium of claim 72.
- 79. A method of producing a mutant ATP-PRT protein, having an altered property relative to ATP-PRT protein, comprising,
a) constructing a three-dimensional structure of ATP-PRT protein having structural coordinates selected from the group consisting of the structural coordinates of a crystalline protein of claim 68, the structural coordinates of FIG. 4 or 5, and the structural coordinates of a protein having a root mean square deviation of the alpha carbon atoms of said protein of less than 2.0 Å when compared to the structural coordinates of FIG. 4 or 5; b) using modeling methods to identify in the three-dimensional structure at least one structural part of the ATP-PRT protein molecule wherein an alteration in said structural part is predicted to result in said altered property; c) providing a nucleic acid molecule coding for a ATP-PRT mutant protein having a modified sequence that encodes a deletion, insertion, or substitution of one or more amino acids at a position corresponding to said structural part; and d) expressing said nucleic acid molecule to produce said mutant; wherein said mutant has at least one altered property relative to the parent.
- 80. A method of producing a mutant ATP-PRT protein, having an altered property relative to ATP-PRT protein, comprising,
a) constructing a three-dimensional structure of a molecule comprising a binding pocket, wherein said binding pocket comprises at least three amino acids selected from the group consisting of Lys9, Arg46, Glu135, Asp148, Asp49, and Glu71, having the structural coordinates of FIG. 4 or 5, or the structural coordinates of a binding pocket homolog, wherein said the root mean square deviation of the backbone atoms of the amino acid residues of said binding pocket and said binding pocket homolog is less than 2.0 Å; b) using modeling methods to identify in the three-dimensional structure at least one portion of said binding pocket wherein an alteration in said portion is predicted to result in said altered property; c) providing a nucleic acid molecule coding for a mutant ATP-PRT protein having a modified sequence that encodes a deletion, insertion, or substitution of one or more amino acids at a position corresponding to said portion; and d) expressing said nucleic acid molecule to produce said mutant; wherein said mutant has at least one altered property relative to the parent.
- 81. A method of producing a computer readable database containing the three-dimensional molecular structural coordinates of a compound capable of binding the active site or binding pocket of a protein molecule, said method comprising
a) introducing into a computer program a computer readable database produced by claim 1;b) generating a three-dimensional representation of the active site or binding pocket of said ATP-PRT protein in said computer program; c) superimposing a three-dimensional model of at least one binding test compound on said representation of the active site or binding pocket; d) assessing whether said test compound model fits spatially into the active site or binding pocket of said ATP-PRT protein; e) assessing whether a compound that fits will fit a three-dimensional model of another protein, the structural coordinates of which are also introduced into said computer program and used to generate a three-dimensional representation of the other protein; and f) storing the three-dimensional molecular structural coordinates of a model that does not fit the other protein into a computer readable database.
- 82. A method for determining whether a compound binds ATP-PRT protein, comprising,
a) providing a computer modeling program with a set of structural coordinates or a three dimensional conformation for a molecule that comprises a binding pocket of ATP-PRT protein, or a homolog thereof; b) providing a said computer modeling program with a set of structural coordinates of a chemical entity; c) using said computer modeling program to evaluate the potential binding or interfering interactions between the chemical entity and said binding pocket; and d) determining whether said chemical entity potentially binds to or interferes with said protein or homolog.
- 83. A method of producing a computer readable database comprising a representation of a compound capable of binding a binding pocket of a ATP-PRT protein, said method comprising,
a) introducing into a computer program a computer readable database produced by claim 1;b) determining a pharmacophore that fits within said binding pocket; c) computationally screening a plurality of compounds to determine which compound(s) or portion(s) thereof fit said pharmacophore; and d) storing a representation of said compound(s) or portion(s) thereof into a computer readable database.
- 84. The method of claim 83, wherein said representation is selected from the group consisting of the compound's name, a chemical or molecular formula of the compound, a chemical structure of the compound, an identifier for the compound, and three-dimensional molecular structural coordinates of the compound.
- 85. The method of claim 83 wherein said binding pocket comprises a binding pocket defined by the structural coordinates of at least three amino acids selected from the group consisting of Lys9, Arg46, Glu135, Asp148, Asp49, and Glu71.
- 86. The method of claim 85 wherein said binding pocket comprises Lys9, Arg46, Glu135, and Asp148 according to the sequence of FIG. 4 or 5.
- 87. The method of claim 86, wherein said binding pocket further comprises Asp49 and Glu71 according to the sequence of FIG. 4 or 5.
- 88. The method of claim 83, wherein said binding pocket comprises an active site.
- 89. A computer readable database produced by claim 83.
- 90. A method comprising electronic transmission of all or part of the computer readable database produced by claim 83.
- 91. A method of producing a computer readable database comprising a representation of a compound capable of binding a binding pocket of a ATP-PRT protein, said method comprising
a) introducing into a computer program a computer readable database produced by claim 1;b) determining a chemical moiety that interacts with said binding pocket; c) computationally screening a plurality of compounds to determine which compound(s)comprise said moiety as a substructure of said compound(s); and d) storing a representation of said compound(s) that comprise said substructure into a computer readable database.
- 92. The method of claim 91, wherein said representation is selected from the group consisting of the compound's name, a chemical or molecular formula of the compound, a chemical structure of the compound, an identifier for the compound, and three-dimensional molecular structural coordinates of the compound.
- 93. The method of claim 91 wherein said binding pocket comprises a binding pocket defined by the structural coordinates of at least three amino acids selected from the group consisting of Lys9, Arg46, Glu135, Asp148, Asp49, and Glu71.
- 94. The method of claim 93 wherein said binding pocket comprises Lys9, Arg46, Glu135 and Asp148 according to the sequence of FIG. 4 or 5.
- 95. The method of claim 94, wherein said binding pocket further comprises Asp49 and Glu71 according to the sequence of FIG. 4 or 5.
- 96. The method of claim 91, wherein said binding pocket comprises an active site.
- 97. A computer readable database produced by claim 91.
- 98. A method comprising electronic transmission of all or part of the computer readable database produced by claim 91.
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims benefit of priority from U.S. Provisional Patent Application Serial No. 60/341,986, filed Dec. 18, 2001, which is hereby incorporated by reference as if set forth in its entirety.
Provisional Applications (1)
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Number |
Date |
Country |
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60341986 |
Dec 2001 |
US |