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Document Figure 1 Diagram of cAPK fold. (a) Stereo MOLSCRIPT diagram. (b) The key loops are as follows: phosphate anchor located between strand 1 and strand 2, catalytic loop located between strands 6 and 7, DFG motif located between strands 8 and 9, activation loop including P+1 site between strand 9 and helix F. Phosphorylation site Thr197 is indicated by a large circle, inhibitor PKI (5–24) is colored in dark, and the P site in the peptide is shown in the dark circle. This figure has been generated using MOLSCRIPT [27]. Page 215 Following the connectivity diagram, helix A is connected to β-strand 1, then to the phosphate anchor encompassing signature motif Gly50XGly 52XXGly55. The β-strand 2 is followed by β-strand 3 carrying invariant Lys72. Three antiparallel beta strands create the unique fold of the nucleotide binding site of the protein kinase. The β-strands 3 is followed by helix B, which is present only in cAPK, helix C, and β-strands 4 and 5. Helix C shows the largest displacements among many different protein kinase structures and consists of invariant Glu91, which forms a salt bridge with Lys72. This salt bridge is absent in the inactive CDK-2 structure [1] but present in the crystal structure of the complex of CDK-2 and its activator-cyclin [7]. Displacement of helix C is perhaps most pronounced in the case of the insulin receptor tyrosine kinase structure (IRK) [3]. In PKA, Phe185 resides in the hydrophobic pocket formed by the hydrophobic residues of helix C (upper lobe) and Tyr164 (lower lobe). In the IRK crystal structure, the hydrophobic residues of helix C, which provide the pocket for invariant Phe185 (of DFG motif), no longer interact with http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_215.html [4/5/2004 5:06:47 PM]
Document Figure 1 (Continued) this residue. The DFG motif in IRK occupies the ATP site, which blocks the access of ATP. Page 216 The division between the upper and lower lobes of the enzyme is well defined by the two major conformations of the upper lobe observed in the crystal structures of cAPK. One conformation has been observed in the orthorhombic crystals of recombinant cAPK [9,10,14] and another in the cubic http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_216.html (1 of 2) [4/5/2004 5:06:54 PM]
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Structure-based Drug Design 14 Stru
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Document 2 Structural Studies of HI
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Document dine (3TC), and 2',3'-dide
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Document monophosphate analogs whic
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Document Analysis of various HIV-1
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Document Page 54 Table 2) [12,54].
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Document Page 56 It is also attract
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Document Table 3 HIV-1 RT Amino Aci
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Document ever, once an NNRTI is bou
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Document Page 65 cal properties of
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Document Page 67 Biochemical data s
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Document Chris Tantillo. The work i
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Document Page 72 16. Goldman ME, Nu
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Document 30. Coffin JM. HIV populat
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Document 45. Majumadar C, Abbotts J
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Document reverse transcriptase inhi
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Document 75. Ring CS, Sun E, McKerr
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Document 89. Hughes SH, Arnold E, H
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Document 106. Cirino NM, Cameron CE
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Document 122. Marshall WS, Beaton G
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Document dine) and didanosine (dide
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Document 149. Craig JC, Duncan IB,
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Document 163. Lacey SF, Larder BA.
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Document Figure 1 Retroviral lifecy
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Document Figure 2 In vivo reactions
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Document Page 88 transfer (Figure 3
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Document Page 92 The role of the N-
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Document Figure 6 Molscript stereo
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Document Page 96 region in the HIV-
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Document day junction resolving enz
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Document -62° for HIV-1 integrase,
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Document Figure 8 Molscript stereo
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Document Page 106 on the same ring
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Document Page 108 mulate during tre
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Document when metals are bound. Fin
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Document cubation of phosphotyrosin
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Document 44. Cushman M, Sherman P.
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Document 65. Gallay P, Swingler S,
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Document 4 Bradykinin Receptor Anta
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Document Page 121 Nearly all cells
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Document Page 123 were poorly satis
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Document Page 125 binding site on t
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Document Page 127 The des-Arg 9 for
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Document Page 129 tolerated by the
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Document receptor, it has not yet b
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Document Page 133 This initial stag
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Document Page 135 might be jointly
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Document Page 137 observed for the
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Document Figure 6 Rat and human B2
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Document Page 141 receptor with int
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Document Figure 9 Composition of te
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Document B. Pharmacology Figure 1 T
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Document We determined the structur
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Document Figure 3 Previously known
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Document large solvent channels and
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Document IV. Drug Design Progressio
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Document position eight from formin
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Document Table 1 Inhibition Data fo
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Document Page 166 As predicated, th
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Document References 1. Parks RE Jr.
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Document 17. Ealick SE, Rule SA, Ca
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Document 6 Structural Implications
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Document Figure 1 A ribbon model of
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Page 221 and 222: Document Page 182 (SAR) model. The
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Page 227 and 228: Document 5. Willenbrock F, Murphy G
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Page 231 and 232: Document Page 189 36. Bode W, Reine
Page 233 and 234: Document 7 Structure—Function Rel
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Page 241 and 242: Document Important for the validity
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Page 247 and 248: Document Page 202 269, and valine-2
Page 249 and 250: Document Figure 6 Structure of α h
Page 251 and 252: Document Page 205 enzyme and of phe
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Page 257 and 258: Document 29. Baker ME. Genealogy of
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Page 267 and 268: Document Page 218 The catalytic loo
Page 269 and 270: Document Page 220 conserved substra
Page 271 and 272: Document Figure 3 (a) Ternary compl
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Page 275 and 276: Document protein kinase core is ess
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Page 281 and 282: Document 9 Structural Studies of Al
Page 283 and 284: Document diverse ARIs have been sho
Page 285 and 286: Document Figure 3 C α trace of the
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Page 291 and 292: Document Figure 7 Stereo of zopolre
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Page 311 and 312: Document Cyclotheonamide A (CtA), a
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Document balance its pro- and antic
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Document Figure 2 Factor Xa structu
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Document Table 2 Naturally Occurrin
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Document Lys in the P1 position is
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Document Figure 11 dArg-ATS 32-38 m
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Document 12 Polypeptide Modulators
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Document C. Specificity Figure 4 Th
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Document IV. Rational Drug Design F
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Document 17. Szelke M. Chemistry of
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Document 34. Rosenberg SH, Plattner
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Document Table 1 Known Three-Dimens
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Document Page 398 with growth hormo
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Document All effects of the IL-1 fa
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Document Page 412 ture is unlike ot
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Document Figure 11 Functional resid
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Document Figure 13 The identified p
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Document B. Interleukin-1 Receptor
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Document Page 423 American Home Pro
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Document Page 427 These aromatic di
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Document 5. Dinarello CA. On the Bi
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Document 39. Saurat JH, Schfferli J
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Document 17 Structure and Functiona
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Document Table 1 Approval Indicatio
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Document Page 438 proteins. One pot
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Document II. Type IFNs A great deal
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Document Page 441 sequence of the m
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Document Page 443 that allowed for
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Document Figure 4 Stereo view of IF
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Document Figure 5 Velcro-key model
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Document Figure 6 Proposed receptor
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Document Page 451 with the cytoplas
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Document for directed subcellular t
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Document Page 462 strains of influe
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Document B. Protein Structure Page
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Document Figure 5 (a) Stereo image
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Document Page 471 molecules in the
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Document hydroxy, and 6 Neu5Ac2en -
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Document Figure 8 Stereo image of t
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Document Page 476 nM, respectively.
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Document Page 478 lished—was asso
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Document VI. Conclusion Page 480 It
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Document 21. Both GW, Sleigh MJ, Co
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Document 45. Varghese JN, Laver WG,
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Document 64. Ward CW, Elleman TC, A
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Document 80. Suzuki Y, Sato K, Kiso
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Document Page 488 against most of t
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Document A. The Canyon Page 491 The
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Document Subsequent studies have sh
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Document Page 495 of the RNA and pr
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Document Figure 4 A ribbon diagram
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Document Figure 5 Some compounds wh
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Document Figure 7 HRV14 VP1 hydroph
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Document C. Structure-Activity Rela
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Document Page 518 The differences b
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Document Page 545 protein binding s
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Document 30. O'Shea EK, Rutkowski R
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Document Acknowledgments Page 620 I
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Document 18. Sawyer TK. In: Peptide
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Document 78. Rodriguez M, Crosby R,
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Document Page 626 SJ, Ogden RC, Red
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Document Med Biol 1991; 306:9-21; (
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Document Page 629 ML, Clare M, Decr
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Document Page 631 197. Musil D, Zuc
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Document Cyclotheonamide A (CtA), 2
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Document D ddI, 152 tumour necrosis
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Document antistasin peptides, 281 c
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Document fragment-based programs, 5
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Document [Human immunodeficiency vi
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Document overview, 103-104, 108-109
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Document [Inhibitors] 2-((3,4-dihyd
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Document antagonistic activity, 416
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Document [Interleukin-1] homology w
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Document Kininogen, 119 high molecu
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Document Matrix-metalloproteinase (
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Document RT inhibitor, 41, 56 Nonpe
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Document Phosphoglycerate kinase (P
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Document [Protease targets] serinyl
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