Claims
- 1. A crystal of a protein-ligand complex comprising a protein-ligand complex of a truncated Ick and a ligand, wherein the crystal effectively diffracts X-rays for the determination of the atomic coordinates of the protein-ligand complex to a resolution of greater than 5.0 Angstroms; and wherein the truncated lck: (a) comprises amino acids 225 to 508 of SEQ ID NO: 1 or an amino acid sequence that differs from amino acids 225 to 508 of SEQ ID NO: 1 by only conservative substitutions; and (b) retains the globular core of the corresponding full-length Ick.
- 2. The crystal of claim 1, wherein the truncated Ick comprises an amino acid sequence of amino acids 251 to 371 of SEQ ID NO: 1, or an amino acid sequence that differs from amino acids 251 to 371 of SEQ ID NO: 1 by only conservative substitutions.
- 3. The crystal of claim 1 or 2, wherein the ligand is staurosporine.
- 4. The crystal of claim 3 having space group of P212121 and a unit cell of dimensions of a=42.2 Å, b=73.8 Å, and c=91.4 Å.
- 5. The crystal of claim 3 having space group of P212121 and a unit cell of dimensions of a=61.5 Å, b=69.0 Å, and c=73.7 Å.
- 6. The crystal of claim 1 wherein the kinase has secondary structural elements that include five beta strands and one helix in the N-terminal lobe (strands 1, 2, 3, 4 and 5 and alpha helix C), and two beta strands and seven alpha helices in the C-terminal domain (strands 6 & 8, and alpha helices D, E, EF, F, G, H and I).
- 7. A method of using the crystal of claim 1 in a inhibitor screening assay comprising:
(a) selecting a potential inhibitor by performing rational drug design with the three-dimensional structure determined for the crystal, wherein said selecting is performed in conjunction with computer modeling; (b) contacting the potential inhibitor with a kinase; and (c) detecting the ability of the potential inhibitor for inhibiting the kinase.
- 8. The method of claim 11, wherein detecting the ability of the potential inhibitor for inhibiting the kinase in step (c) is performed using an enzyme inhibition assay.
- 9. The method of claim 11, wherein detecting the ability of the potential inhibitor for inhibiting the kinase in step (c) is performed using a cellular- based assay.
- 10. The method of claim 11 further comprising:
(d) growing a supplemental crystal comprising a protein-ligand complex formed between the kinase and a first potential inhibitor from step (a), wherein the supplemental crystal effectively diffracts X-rays for the determination of the atomic coordinates of the protein-ligand complex to a resolution of greater than 5.0 Angstroms; (e) determining the three-dimensional structure of the supplemental crystal; (f) selecting a second potential inhibitor by performing rational drug design with the three-dimensional structure determined for the supplemental crystal, wherein said selecting is performed in conjunction with computer modeling; (g) contacting the second potential inhibitor with a kinase; and (h) detecting the ability of the second potential inhibitor for inhibiting the kinase.
- 11. A method for identifying a potential inhibitor of a kinase comprising:
(a) selecting or designing a potential inhibitor by performing rational drug design with the three-dimensional structure coordinates of any of Tables 1-5, wherein said selecting is performed in conjunction with computer modeling; (b) contacting the potential inhibitor with a kinase; and (c) detecting the ability of the potential inhibitor for inhibiting the kinase.
- 12. The method of claim 15, wherein detecting the ability of the potential inhibitor for inhibiting the kinase in step (c) is performed using an enzyme inhibition assay.
- 13. The method of claim 15, wherein detecting the ability of the potential inhibitor for inhibiting the kinase in step (c) is performed using a cellular-based assay.
- 14. The method of claim 15, wherein the potential inhibitor is designed de novo.
- 15. The method of claim 15, wherein the potential inhibitor is designed from a known inhibitor.
- 16. The method of claim 15 further comprising:
(d) selecting an second potential inhibitor by performing rational drug design with the three-dimensional structure coordinates of any of Tables 1-5 and the potential inhibitor of step (a), wherein said selecting is performed in conjunction with computer modeling; (e) contacting the potential inhibitor with a kinase; and (f) detecting the ability of the potential inhibitor for inhibiting the kinase.
- 17. A method of using truncated Ick to grow a crystal of a protein-ligand complex comprising:
(c) contacting truncated Ick with a ligand, wherein the truncated Ick forms a protein-ligand complex with the ligand; and (d) growing the crystal of the protein-ligand complex; wherein the crystal effectively diffracts X-rays for the determination of the atomic coordinates of the protein-ligand complex to a resolution of greater than 5.0 Angstroms.
- 18. The method of claim 21, wherein said growing is performed by hanging drop vapor diffusion.
- 19. The method of claim 21, wherein said ligand is staurosporine.
- 20. A method of growing a crystal of a truncated Ick-ligand complex wherein the crystal effectively diffracts X-rays for the determination of the atomic coordinates of the protein-ligand complex to a resolution of greater than 5.0 Angstroms, comprising:
(a) contacting a truncated Ick solution with a ligand, wherein the truncated Ick forms a protein-ligand complex with the ligand; and (b) growing the crystal of the protein-ligand complex; wherein the crystal effectively diffracts X-rays for the determination of the atomic coordinates of the protein-ligand complex to a resolution of greater than 5.0 Angstroms.
- 21. The method of claim 25, wherein the growing is performed by hanging drop vapor diffusion.
- 22. The method of claim 25, wherein the ligand is staurosporine.
- 23. A method of producing a crystal of a truncated Ick-ligand complex wherein the crystal effectively diffracts X-rays for the determination of the atomic coordinates of the protein-ligand complex to a resolution of greater than 5.0 Angstroms, comprising contacting a truncated Ick crystal with a ligand, wherein the truncated Ick forms a protein-ligand complex with the ligand within the crystal, and wherein the crystal effectively diffracts X-rays for the determination of the atomic coordinates of the protein-ligand complex to a resolution of greater than 5.0 Angstroms.
- 24. The method of claim 28, wherein the ligand is staurosporine.
- 25. A method of using the three-dimensional structure coordinates of any one of Tables 1-5, comprising:
(a) Determining structure factors from the coordinates; and (b) Applying said structure factor information to a set of X-ray diffraction data obtained from a crystal of a protein homologous to SEQ ID NO: 1; (c) Solving the three-dimensional structure of the protein homologous to SEQ ID NO: 1.
- 26. A computer readable data storage material encoded with computer readable data comprising structure coordinates of any one or more of Tables 1-5.
- 27. A computer readable data storage material encoded with computer readable data comprising structure coordinates of the active site of any one or more of Tables 1-5.
- 28. A method for identifying a potential inhibitor of a kinase comprising:
(a) selecting or designing a potential inhibitor by performing rational drug design with a computer readable data storage material encoded with computer readable data comprising structure coordinates of any one or more of Tables 1-5, wherein said selecting is performed in conjunction with computer modeling; (b) contacting the potential inhibitor with a kinase; and (c) detecting the ability of the potential inhibitor for inhibiting the kinase.
- 29. A polynucleotide sequence encoding the polypeptide comprising residues 235-501 of SEQ ID NO.: 1, and further comprising the sequence Arg-His-His-His-His-His-His attached to residue 501 and methionine attached to residue 235, or having conservative substitutions thereof.
- 30. An expression vector containing the polynucleotide sequence of claim 29.
- 31. A host cell containing the vector of claim 29.
- 32. An isolated polypeptide comprising residues 235-501 of SEQ ID NO.: 1, and further comprising the sequence Arg-His-His-His-His-His-His attached to residue 501 and methionine attached to residue 235, or having conservative substitutions thereof.
- 33. An isolated polypeptide made by a method comprising the steps of:
(d) Introducing a recombinant nucleic acid encoding a polypeptide comprising residues 235-501 of SEQ ID NO.: 1, and further comprising the sequence Arg-His-His-His-His-His-His attached to residue 501 and methionine attached to residue 235, or having conservative substitutions thereof, into a host cell or cellular extract; (e) Incubating the host cell or cellular extract under conditions whereby the polypeptide is expressed; and (f) Isolating the polypeptide.
- 34. Use of an isolated polypeptide comprising residues 235-501 of SEQ ID NO.:1 and further comprising the sequence Arg-His-His-His-His-His-His attached to residue 501 and methionine attached to residue 235, or having conservative substitutions thereof, for growing polypeptide:inhibitor complexes comprising contacting said polypeptide with a chemical compound.
- 35. The use of claim 34, wherein the chemical compound is a kinase inhibitor.
- 36. A method for obtaining activated Lck of high homogeneity suitable for crystallization studies, comprising the steps of:
(a) contacting a stabilizer with a polypeptide comprising residues 235-501 of SEQ ID NO.: 1, and further comprising the sequence Arg-His-His-His-His-His-His attached to residue 501 and methionine attached to residue 235, or having conservative substitutions thereof, (b) isolating the polypeptide comprising residues 235-501 of SEQ ID NO.: 1, and further comprising the sequence Arg-His-His-His-His-His-His attached to residue 501 and methionine attached to residue 235, or having conservative substitutions thereof, from unphosphorylated and multi-phophorylated variants thereof.
- 37. The method of claim 36, wherein the stabilizer is a polyol.
- 38. A stabilized form of activated Lck of high homogeneity suitable for crystallization studies, comprising (a) a polypeptide comprising residues 235-501 of SEQ ID NO.: 1, and further comprising the sequence Arg-His-His-His-His-His-His attached to residue 501 and methionine attached to residue 235, or having conservative substitutions thereof, and (b) a kosmotropes.
- 39. The activated Lck of method 38, further comprising (c) an additional stabilizing agent.
Parent Case Info
[0001] This application is a continuation of U.S. patent application Ser. No. 09/574,559, filed May 19, 2000, which claims priority benefit under Title 35 USC §119(e) of U.S. Provisional Application No. 60/134,965, filed May 19, 1999 and entitled Crystal of a Kinase-Ligand Complex and Methods of Use, the entire contents of which are incorporated herein by reference.
Provisional Applications (1)
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Number |
Date |
Country |
|
60134965 |
May 1999 |
US |
Continuations (1)
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Number |
Date |
Country |
Parent |
09574559 |
May 2000 |
US |
Child |
10798156 |
Mar 2004 |
US |