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Document Table 3 Some Known 3D <strong>Structure</strong>s of Signal-Transduction Proteins (Apo/Complexes) Protein Target Apo/Complex Resolution Reference Src homology domains Abl SH2 —(Apo) NMR 238 Src SH2 —(Apo) 2.5 Å 239 phosphopeptide 2.7 Å 239 phosphopeptide NMR 240 PLC (C) SH2 phosphopeptide NMR 241 Shc SH2 phosphopeptide NMR 242 Lck SH2 phosphopeptide 2.2 Å 243a p85 (N) SH2 phosphopeptide 2.0 Å 244 Syp SH2 phosphopeptide 2.0 Å 245 Grb2 SH2 phosphopeptide 2.1 Å 246 Syk SH2 phosphopeptide NMR 247 Zap70 SH2-SH2 phosphopeptide (tandem) 1.9 Å 248 Src SH3 —(Apo) NMR 249a peptide NMR 249b Abl SH3 peptide 2.0 Å 250 Crk SH3 peptide 1.5 Å 251 Grb2 SH3 peptide NMR 252 Grb2 SH3-SH2-SH3 —(Apo) 3.1 Å 253 Tyr and Ser/Thr kinases Insulin receptor Tyr kinase —(Apo) 2.1 Å 254 cAMP-dep. protein kinase —(Apo) 3.9 Å 255 http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_613.html (1 of 2) [4/9/2004 1:39:56 AM] Page 613
Document (Ser/Thr) peptide 2.9 Å 255 Cell cycle-dep. protein —(Apo) 2.4 Å 256a kinase (CDK2) protein (p27 Kip1 inhibitory domain) 2.3 Å 256b Mitogen-activated protein kinase (MAPK) Tyr and Ser/Thr phosphatases —(Apo) 2.3 Å 257 BH-PTP (Tyr) —(Apo) 2.2 Å 258a PTP1B (Tyr) —(Apo) 2.8 Å 258b peptide (C215S mutant enzyme) 2.6 Å 258c VH1 (Tyr and Ser/Thr”) —(Apo) 2.1 Å 259 PP-1 (Ser/Thr) —(Apo) 2.1 Å 260 pTyr binding domains IRS-1 PTB —(Apo) 1.95 Å 261 peptide 1.8 Å 261 IRS-1 PTB peptide NMR 262 Pro cis-trans isomerases Cyclophilin peptide (cyclosporin-A) 2.8 Å 263 FKBP-12 FK-506 (macrolide antibiotic) 1.7 Å 264 http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_613.html (2 of 2) [4/9/2004 1:39:56 AM]
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Structure-based Drug Design 14 Stru
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Document Page 15 Thiazoles are less
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Document Figure 5 Stereo view AG134
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Document Figure 7 Cartoon represent
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Document Page 33 sustained in many
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Document 8. Kaplan AH, Zack JA, Kni
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Document 22. Krausslich HG, Ingraha
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Document 47. Tummino PJ, Ferguson D
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Document 60. Condra JH, Schleif WA,
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Document 74. Reddy RM, Varney MD, K
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Document 2 Structural Studies of HI
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Document Figure 1 (a) Chemical stru
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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 61 now clear that the
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Document Page 63 most of the amino
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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 Page 69 determining the me
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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 Page 101 crystallized unde
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Document Figure 8 Molscript stereo
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Document proposed mechanisms. For e
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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 4. Vink C, Plasterk RHA. T
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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 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 16. Martorana PA, Kettenba
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Document 39. Mavunkel BJ, Lu Z, Kyl
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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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Document Page 176 0.43 Å) as the c
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Document Page 178 studies show that
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Document Figure 5 (a) A cut away vi
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Document Page 182 (SAR) model. The
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Document IX. S2' Interactions Page
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Document Figure 6 (a) The pocket of
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Document 5. Willenbrock F, Murphy G
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Document 20. Murphy G, Docherty AJP
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Document Page 189 36. Bode W, Reine
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Document 7 Structure—Function Rel
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Document Figure 1 Reactions catalyz
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Document Figure 2 Structure of lico
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Document Figure 3 (Continued) Page
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Document Important for the validity
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Document Figure 4 Amino acids impor
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Document III. Results and Discussio
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Document Page 202 269, and valine-2
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Document Figure 6 Structure of α h
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Document Page 205 enzyme and of phe
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Document Page 207 sure and the acti
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Document 13. Wilson RC, Krozowski Z
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Document 29. Baker ME. Genealogy of
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Document Page 214 viruses. Specific
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Document Figure 1 (Continued) this
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Document Page 218 The catalytic loo
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Document Page 220 conserved substra
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Document Figure 3 (a) Ternary compl
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Document Figure 5 (a) Staurosporine
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Document protein kinase core is ess
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Document 24. Madhusudan Xuong N-H,
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Document 9 Structural Studies of Al
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Document diverse ARIs have been sho
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Document Figure 3 C α trace of the
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Document Figure 4 Surface represent
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Document Figure 7 Stereo of zopolre
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Document B. Structures Figure 8 Seq
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Document This method was used to sc
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Document 2. Lee AYW, Chung SK, Chun
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Document 18. Wilson DK, Tarle I, Pe
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Document 35. Pailhoux EA, Martinez
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Document 10 Structure-Based Design
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Document Cyclotheonamide A (CtA), a
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Document Page 256 The discovery pro
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Document balance its pro- and antic
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Document Figure 1 The coagulation c
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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 A. Chemical Modification P
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Document 13 Rational Design of Reni
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Document Page 323 been suggested th
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Document plasma. This may arise fro
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Document C. Specificity Figure 4 Th
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Document Figure 5 The S 3 specifici
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Document IV. Rational Drug Design F
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Document 2. Blundell TL, Cooper J,
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Document 17. Szelke M. Chemistry of
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Document 34. Rosenberg SH, Plattner
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Document Page 343 14 Structural Asp
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Document Figure 2 The reaction cata
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Document Figure 4 Amino acid sequen
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Document Figure 5 Schematic stereo
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Document Figure 8 The catalytic mac
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Document Figure 10 Structures of so
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Document Figure 1 Available drugs f
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Document Table 1 Trypanosomal Targe
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Document II. Three Glycolytic Enzym
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Document Figure 12 Predicted bindin
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Document 65. João HC, Williams RJP
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Document 84. Verlinde CLMJ, Hol WGJ
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Document 16 Progress in the Design
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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 405 strands constitut
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Document Figure 4 (a) Stereo diagra
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Document Figure 6 (a) Stereo diagra
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Document Figure 7 (a) Superposition
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Document Page 412 ture is unlike ot
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Document Figure 10 Schematic diagra
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Document Page 416 positions of the
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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 425 Antinflammatory D
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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 21. Seckinger P, Lowenthal
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Document 39. Saurat JH, Schfferli J
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Document receptor antagonist into a
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Document 74. Bender PE, Lee JC., ed
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Document 102. Machin PJ, Osbond JM,
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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 Page 464 could not again b
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Document Figure 3 (a) A MOLSCRIPT [
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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 40. Drzenick R, Frank H, R
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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 486 95. Ryan DM, Tice
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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 Hydrophobicity Requirement
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Document Figure 9 A solvent-accessi
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Document accommodate a variety of d
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Document Figure 10 Possible hydroge
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Document Page 514 sis. Large number
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Document conformational transition
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Document Page 527 function. Iterati
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Document Figure 3 Generation of com
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Document Page 530 screen. For examp
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Document 17. Zuckermann RN, Martin
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Document 21 Structure-Based Combina
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Document Figure 8 Minimized structu
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Document 10. Bobbyer DNA, Goodford
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Document 30. O'Shea EK, Rutkowski R
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Page 707 and 708: Document Page 569 molecule. A nonco
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Page 715 and 716: Document Figure 12 Peptide scaffold
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Page 735 and 736: Document Page 595 the MC1 receptor
Page 739 and 740: Document Figure 22 Protease 3D stru
Page 741 and 742: Document Page 601 inhibitors 100 [1
Page 743 and 744: Document Page 603 hydroxymethyl sub
Page 745 and 746: Document Page 605 For other serinyl
Page 747 and 748: Document Page 607 scopic studies pr
Page 749 and 750: Document Page 609 (e.g., thermolysi
Page 751 and 752: Document Figure 28 Protease 3D stru
Page 753: Document Figure 29 Protease 3D stru
Page 761 and 762: Document Page 617 Val (131) showed
Page 763 and 764: Document Figure 32 PTP and PTB 3D s
Page 765 and 766: Document Acknowledgments Page 620 I
Page 767 and 768: Document 18. Sawyer TK. In: Peptide
Page 769 and 770: Document Page 622 Fukuroda T, Fukam
Page 771 and 772: Document Page 623 53. Bird J, Harpe
Page 773 and 774: Document 78. Rodriguez M, Crosby R,
Page 775 and 776: Document MA, Welch KM, Hallak H, Ta
Page 777 and 778: Document Page 626 SJ, Ogden RC, Red
Page 779 and 780: Document 97; (e) Fujii I, Nakamura
Page 781 and 782: Document Med Biol 1991; 306:9-21; (
Page 783 and 784: Document Page 629 ML, Clare M, Decr
Page 785 and 786: Document Page 630 177. (a) Bode W,
Page 787 and 788: Document Page 631 197. Musil D, Zuc
Page 789 and 790: Document son AH, Drummond AH, Huxle
Page 791 and 792: Document 236. (a) Marshall MS. TIBS
Page 795 and 796: Document 274. (a) Kavanaugh WM, Wil
Page 797 and 798: Document replacements, 563-565 1-am
Page 799 and 800: Document inhibitor binding, 323, 33
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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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