| US 7,558,717 B2 | ||
| Crystal structure of human JAK3 kinase domain complex and binding pockets thereof | ||
| Harmon Zuccola, Westwood, Mass. (US); Marc Jacobs, Boston, Mass. (US); Lovorka Swenson, Belmont, Mass. (US); and Kumkum Saxena, Framingham, Mass. (US) | ||
| Assigned to Vertex Pharmaceuticals Incorporated, Cambridge, Mass. (US) | ||
| Filed on Apr. 26, 2005, as Appl. No. 11/114,979. | ||
| Claims priority of provisional application 60/669771, filed on Apr. 08, 2005. | ||
| Claims priority of provisional application 60/566393, filed on Apr. 28, 2004. | ||
| Prior Publication US 2006/0030018 A1, Feb. 09, 2006 | ||
| Int. Cl. C12Q 1/00 (2006.01); C12Q 1/48 (2006.01); G01N 33/53 (2006.01); G01N 31/00 (2006.01); C12N 9/00 (2006.01); C12N 9/12 (2006.01); G06G 7/58 (2006.01) | ||
| U.S. Cl. 703—11 [435/7.6; 435/7.71; 435/15; 435/183; 435/194; 435/4; 702/27] | 8 Claims |
| 1. A method of designing a compound or complex that interacts with a binding pocket or domain selected from the group consisting
of:
(i) human Janus Kinase 3 amino acid residues Gln827, Leu828, Gly829, Lys830, Gly831, Asn832, Phe833, Gly834, Ser835, Val836,
Glu837, Leu838, Val852, Ala853, Val854, Lys855, Gln856, Leu857, Val884, Lys885, Tyr886, Leu900, Val901, Met902, Glu903, Tyr904,
Leu905, Pro906, Ser907, Gly908, Cys909, Leu910, Arg911, Asp912, His947, Asp949, Leu950, Ala951, Ala952, Arg953, Asn954, Ile955,
Leu956, Val957, Ala966, Asp967, Leu970, Glu985, Gln988, Ser989, Pro990 and Trp993 according to Table 2; and
(ii) human Janus Kinase 3 amino acid residues according to Table 2;
comprising the steps of:
(a) producing a crystal of human Janus Kinase 3 in complex with AMP-PNP, wherein said human Janus Kinase 3 consists of amino
acid residues 810-1115 of SEQ ID NO: 1, wherein said crystal is characterized with space group P21 and has unit cell parameters of a=59.98 Å, b=90.19 Å, c=69.00 Å, α=90°, β=111.5°, γ90°;
(b) providing the structure coordinates of said binding pocket or domain of the crystal of step (a), according to Table 2,
on a computer capable of generating three-dimensional structural information from said structure coordinates, wherein the
root mean square deviation of the backbone atoms is not greater than about 2.5 Å;
(c) using the computer to dock a first chemical entity in part of the binding pocket or domain;
(d) docking at least a second chemical entity in another part of the binding pocket or domain;
(e) quantifying the association between the first or second chemical entity and part of the binding pocket or domain;
(f) repeating steps (c) to (e) with another first and second chemical entity, selecting a first and a second chemical entity
based on said quantified association of all of said first and second chemical entity;
(g) optionally, visually inspecting the relationship of the first and second chemical entity to each other in relation to
the binding pocket or domain on a computer screen using the three-dimensional graphical representation of the binding pocket
or domain and said first and second chemical entity; and
(h) assembling the first and second chemical entity into a compound or complex that interacts with said binding pocket or
domain by model building.
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