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Document Figure 3 Stereo ribbon diagram of Factor Xa [4]. Residues of the catalytic triad are shown (His 57 , Asp 102 , Ser 195 ) as well as residues of specific interest for the binding of small molecules to the active site: Glu 192 ; S4 pocket residues Tyr 99 , Phe 174 , Trp 215 ; and S1 pocket residue, Asp 189 . Residues are designated with the chymotrypsin numbering. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_269.html [4/5/2004 5:12:37 PM] Page 269
Document Table 2 Naturally Occurring Inhibitors of Factor Xa Inhibitor Source K i Structural information TFPI Human 3 pM [49] 90 nM [50] Ecotin Escherichia coli 50 pM [44] X-ray; complex with trypsin [46] TAP Ornithidoros moubata (tick) 135 pM [13] 2D-NMR [57,58] Antistasin Haementeria officinalis (leech) 61 pM [51] (X-ray in progress) [52] AcAP5 Ancylostoma caninum 43 pM [19] homology to Ascaris lumbricoides var.suum [79,80] Page 270 Studies of these natural inhibitors can be useful in defining the active site requirements for Factor Xa inhibition, and importantly, can indicate the level of inhibition that may be necessary for an effective Factor Xa inhibitor, recognizing that TAP and antistasin have evolved to yield functional, in vivo antithrombotics. Table 3 shows the reactive-site sequences of these substratelike inhibitors as well as the cleavage site sequences recognized <strong>by</strong> Factor Xa in the activation of prothrombin (PT), Factor VII, and Factor V. A. Tissue Factor Pathway Inhibitor (TFPI) The mature tissue factor pathway inhibitor (TFPI) is a 276-residue protein consisting of three tandom domains with homology to the Kunitz-like protease http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_270.html (1 of 2) [4/5/2004 5:12:45 PM]
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Structure-based Drug Design 14 Stru
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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 Figure Continued Page 45 r
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Document Figure 2 Ribbon diagrams o
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Document Figure 3 Overall structure
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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 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 Page 115 21. Kulkosky J, J
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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 125 binding site on t
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Document Page 127 The des-Arg 9 for
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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 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 218 The catalytic loo
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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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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 289 and 290: Document Figure 5 Schematic represe
Page 291 and 292: Document Figure 7 Stereo of zopolre
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Page 295 and 296: Document This method was used to sc
Page 297 and 298: Document 2. Lee AYW, Chung SK, Chun
Page 299 and 300: Document 18. Wilson DK, Tarle I, Pe
Page 301 and 302: Document 35. Pailhoux EA, Martinez
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Page 311 and 312: Document Cyclotheonamide A (CtA), a
Page 313 and 314: Document Page 256 The discovery pro
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Page 319 and 320: Document balance its pro- and antic
Page 321 and 322: Document Page 263 15. Tabernero L,
Page 323 and 324: Document 31. Kettner C, Shaw E. D-P
Page 325 and 326: Document Figure 1 The coagulation c
Page 327: Document Figure 2 Factor Xa structu
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Page 335 and 336: Document Lys in the P1 position is
Page 337 and 338: Document Page 276 In both cases the
Page 339 and 340: Document Page 278 The n=3 chain len
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Page 343 and 344: Document Figure 11 dArg-ATS 32-38 m
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Page 363 and 364: Document 12 Polypeptide Modulators
Page 365 and 366: Document Page 297 whereas, calcium
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Page 373 and 374: Document A. Chemical Modification P
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Document 13 Rational Design of Reni
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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 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 Figure 5 Schematic stereo
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Document Figure 8 The catalytic mac
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Document Figure 1 Available drugs f
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Document Table 1 Trypanosomal Targe
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Document 5-Methoxytryptamine 19.0 9
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Document Figure 12 Predicted bindin
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Document Page 388 nosine proved to
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Document 65. João HC, Williams RJP
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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 Figure 2 Structural alignm
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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 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 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 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 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 Figure 9 A solvent-accessi
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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 518 The differences b
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Document 20 The Integration of Stru
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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 21 Structure-Based Combina
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Document Page 545 protein binding s
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Document Page 555 N-acylpyrrolidine
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Document 10. Bobbyer DNA, Goodford
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Document 30. O'Shea EK, Rutkowski R
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Document Figure 22 Protease 3D stru
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Document Figure 32 PTP and PTB 3D s
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Document Acknowledgments Page 620 I
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Document 18. Sawyer TK. In: Peptide
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Document 97; (e) Fujii I, Nakamura
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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 site, 52, 55, 61 triad, 24
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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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