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PDBsum entry 1r06

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Rhinovirus coat protein PDB id
1r06
Jmol
Contents
Ligands
W35
Superseded by: 2r06
PDB id:
1r06
Name: Rhinovirus coat protein
Structure: Rhinovirus 14 ( HRV 14) complex with antiviral agent WIN 6
Source: Human (homo sapiens) virus grown in he La cells
Authors: J.Badger,T.J.Smith,M.G.Rossmann
Key ref: J.Badger et al. (1988). Structural analysis of a series of antiviral agents complexed with human rhinovirus 14. Proc Natl Acad Sci U S A, 85, 3304-3308. PubMed id: 2835768 DOI: 10.1073/pnas.85.10.3304
Date:
18-Feb-88     Release date:   09-Oct-88    
 Headers
 References

 

 
DOI no: 10.1073/pnas.85.10.3304 Proc Natl Acad Sci U S A 85:3304-3308 (1988)
PubMed id: 2835768  
 
 
Structural analysis of a series of antiviral agents complexed with human rhinovirus 14.
J.Badger, I.Minor, M.J.Kremer, M.A.Oliveira, T.J.Smith, J.P.Griffith, D.M.Guerin, S.Krishnaswamy, M.Luo, M.G.Rossmann.
 
  ABSTRACT  
 
The binding to human rhinovirus 14 of a series of eight antiviral agents that inhibit picornaviral uncoating after entry into host cells has been characterized crystallographically. All of these bind into the same hydrophobic pocket within the viral protein VP1 beta-barrel structure, although the orientation and position of each compound within the pocket was found to differ. The compounds cause the protein shell to be less flexible, thereby inhibiting disassembly. Although the antiviral potency of these compounds varies by 120-fold, they all induce the same conformational changes on the virion. The interactions of these compounds with the viral capsid are consistent with their observed antiviral activities against human rhinovirus 14 drug-resistant mutants and other rhinovirus serotypes. Crystallographic studies of one of these mutants confirm the partial sequencing data and support the finding that this is a single mutation that occurs within the binding pocket.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22472617 J.M.Hogle (2012).
A 3D framework for understanding enterovirus 71.
  Nat Struct Mol Biol, 19, 367-368.  
19368882 D.L.Mobley, and K.A.Dill (2009).
Binding of small-molecule ligands to proteins: "what you see" is not always "what you get".
  Structure, 17, 489-498.  
  19194015 T.F.Lerch, Q.Xie, H.M.Ongley, J.Hare, and M.S.Chapman (2009).
Twinned crystals of adeno-associated virus serotype 3b prove suitable for structural studies.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 177-183.  
18585795 R.Perera, M.Khaliq, and R.J.Kuhn (2008).
Closing the door on flaviviruses: entry as a target for antiviral drug design.
  Antiviral Res, 80, 11-22.  
16510969 F.Fabiola, A.Korostelev, and M.S.Chapman (2006).
Bias in cross-validated free R factors: mitigation of the effects of non-crystallographic symmetry.
  Acta Crystallogr D Biol Crystallogr, 62, 227-238.  
15883190 L.Wang, and D.L.Smith (2005).
Capsid structure and dynamics of a human rhinovirus probed by hydrogen exchange mass spectrometry.
  Protein Sci, 14, 1661-1672.  
16107202 Z.Liu, J.Yuan, B.Yanagawa, D.Qiu, B.M.McManus, and D.Yang (2005).
Coxsackievirus-induced myocarditis: new trends in treatment.
  Expert Rev Anti Infect Ther, 3, 641-650.  
15331736 C.Xiao, T.J.Tuthill, C.M.Bator Kelly, L.J.Challinor, P.R.Chipman, R.A.Killington, D.J.Rowlands, A.Craig, and M.G.Rossmann (2004).
Discrimination among rhinovirus serotypes for a variant ICAM-1 receptor molecule.
  J Virol, 78, 10034-10044.  
15331700 D.Melamed, M.Mark-Danieli, M.Kenan-Eichler, O.Kraus, A.Castiel, N.Laham, T.Pupko, F.Glaser, N.Ben-Tal, and E.Bacharach (2004).
The conserved carboxy terminus of the capsid domain of human immunodeficiency virus type 1 gag protein is important for virion assembly and release.
  J Virol, 78, 9675-9688.  
15064754 N.Verdaguer, I.Fita, M.Reithmayer, R.Moser, and D.Blaas (2004).
X-ray structure of a minor group human rhinovirus bound to a fragment of its cellular receptor protein.
  Nat Struct Mol Biol, 11, 429-434.
PDB code: 1v9u
15452226 Y.Zhang, A.A.Simpson, R.M.Ledford, C.M.Bator, S.Chakravarty, G.A.Skochko, T.M.Demenczuk, A.Watanyar, D.C.Pevear, and M.G.Rossmann (2004).
Structural and virological studies of the stages of virus replication that are affected by antirhinovirus compounds.
  J Virol, 78, 11061-11069.
PDB codes: 1na1 1ncq 1ncr 1nd2 1nd3
14750441 J.Rajcáni (2003).
Molecular mechanisms of virus spread and virion components as tools of virulence. A review.
  Acta Microbiol Immunol Hung, 50, 407-431.  
12384371 S.Höglund, J.Su, S.S.Reneby, A.Végvári, S.Hjertén, I.M.Sintorn, H.Foster, Y.P.Wu, I.Nyström, and A.Vahlne (2002).
Tripeptide interference with human immunodeficiency virus type 1 morphogenesis.
  Antimicrob Agents Chemother, 46, 3597-3605.  
  12079640 V.Kytö, A.Saraste, J.Fohlman, N.G.Ilbäck, H.Harvala, T.Vuorinen, and T.Hyypiä (2002).
Cardiomyocyte apoptosis after antiviral WIN 54954 treatment in murine coxsackievirus B3 myocarditis.
  Scand Cardiovasc J, 36, 187-192.  
11159387 B.Speelman, B.R.Brooks, and C.B.Post (2001).
Molecular dynamics simulations of human rhinovirus and an antiviral compound.
  Biophys J, 80, 121-129.  
11369862 L.Wang, L.C.Lane, and D.L.Smith (2001).
Detecting structural changes in viral capsids by hydrogen exchange and mass spectrometry.
  Protein Sci, 10, 1234-1243.  
11182317 S.K.Tsang, J.Cheh, L.Isaacs, D.Joseph-McCarthy, S.K.Choi, D.C.Pevear, G.M.Whitesides, and J.M.Hogle (2001).
A structurally biased combinatorial approach for discovering new anti-picornaviral compounds.
  Chem Biol, 8, 33-45.  
10651041 B.B.Goldman, and W.T.Wipke (2000).
QSD quadratic shape descriptors. 2. Molecular docking using quadratic shape descriptors (QSDock).
  Proteins, 38, 79-94.  
10611281 A.T.Hadfield, G.D.Diana, and M.G.Rossmann (1999).
Analysis of three structurally related antiviral compounds in complex with human rhinovirus 16.
  Proc Natl Acad Sci U S A, 96, 14730-14735.
PDB codes: 1qju 1qjx 1qjy
  10471549 D.C.Pevear, T.M.Tull, M.E.Seipel, and J.M.Groarke (1999).
Activity of pleconaril against enteroviruses.
  Antimicrob Agents Chemother, 43, 2109-2115.  
10647183 E.Hendry, H.Hatanaka, E.Fry, M.Smyth, J.Tate, G.Stanway, J.Santti, M.Maaronen, T.Hyypiä, and D.Stuart (1999).
The crystal structure of coxsackievirus A9: new insights into the uncoating mechanisms of enteroviruses.
  Structure, 7, 1527-1538.
PDB code: 1d4m
11504496 P.R.Wyde (1999).
Chemotherapy of respiratory viruses: prospects and challenges.
  Drug Resist Updat, 2, 244-258.  
9931028 T.J.Stout, D.Tondi, M.Rinaldi, D.Barlocco, P.Pecorari, D.V.Santi, I.D.Kuntz, R.M.Stroud, B.K.Shoichet, and M.P.Costi (1999).
Structure-based design of inhibitors specific for bacterial thymidylate synthase.
  Biochemistry, 38, 1607-1617.
PDB codes: 1tsl 1tsm
9487732 P.E.Prevelige (1998).
Inhibiting virus-capsid assembly by altering the polymerisation pathway.
  Trends Biotechnol, 16, 61-65.  
9294865 D.Joseph-McCarthy, J.M.Hogle, and M.Karplus (1997).
Use of the multiple copy simultaneous search (MCSS) method to design a new class of picornavirus capsid binding drugs.
  Proteins, 29, 32-58.  
9261087 K.N.Lentz, A.D.Smith, S.C.Geisler, S.Cox, P.Buontempo, A.Skelton, J.DeMartino, E.Rozhon, J.Schwartz, V.Girijavallabhan, J.O'Connell, and E.Arnold (1997).
Structure of poliovirus type 2 Lansing complexed with antiviral agent SCH48973: comparison of the structural and biological properties of three poliovirus serotypes.
  Structure, 5, 961-978.
PDB code: 1eah
9253417 M.W.Wien, S.Curry, D.J.Filman, and J.M.Hogle (1997).
Structural studies of poliovirus mutants that overcome receptor defects.
  Nat Struct Biol, 4, 666-674.
PDB codes: 1al2 1ar6 1ar7 1ar8 1ar9 1asj
9122218 N.Vaidehi, and W.A.Goddard (1997).
The pentamer channel stiffening model for drug action on human rhinovirus HRV-1A.
  Proc Natl Acad Sci U S A, 94, 2466-2471.  
  9174174 P.J.Buontempo, S.Cox, J.Wright-Minogue, J.L.DeMartino, A.M.Skelton, E.Ferrari, R.Albin, E.J.Rozhon, V.Girijavallabhan, J.F.Modlin, and J.F.O'Connell (1997).
SCH 48973: a potent, broad-spectrum, antienterovirus compound.
  Antimicrob Agents Chemother, 41, 1220-1225.  
  8995703 W.Kraus, H.Zimmermann, H.J.Eggers, and B.Nelsen-Salz (1997).
Rhodanine resistance and dependence of echovirus 12: a possible consequence of capsid flexibility.
  J Virol, 71, 1697-1702.  
8939746 R.Zhao, D.C.Pevear, M.J.Kremer, V.L.Giranda, J.A.Kofron, R.J.Kuhn, and M.G.Rossmann (1996).
Human rhinovirus 3 at 3.0 A resolution.
  Structure, 4, 1205-1220.
PDB code: 1rhi
8634279 V.Helms, E.Deprez, E.Gill, C.Barret, G.Hui Bon Hoa, and R.C.Wade (1996).
Improved binding of cytochrome P450cam substrate analogues designed to fill extra space in the substrate binding pocket.
  Biochemistry, 35, 1485-1499.  
  7815487 W.Zauner, D.Blaas, E.Kuechler, and E.Wagner (1995).
Rhinovirus-mediated endosomal release of transfection complexes.
  J Virol, 69, 1085-1092.  
  7966611 A.G.Mosser, J.Y.Sgro, and R.R.Rueckert (1994).
Distribution of drug resistance mutations in type 3 poliovirus identifies three regions involved in uncoating functions.
  J Virol, 68, 8193-8201.  
  7813425 E.Colston, and V.R.Racaniello (1994).
Soluble receptor-resistant poliovirus mutants identify surface and internal capsid residues that control interaction with the cell receptor.
  EMBO J, 13, 5855-5862.  
  7849588 M.G.Rossmann (1994).
Viral cell recognition and entry.
  Protein Sci, 3, 1712-1725.  
7994569 V.L.Giranda (1994).
Structure-based drug design of antirhinoviral compounds.
  Structure, 2, 695-698.  
  8382293 A.G.Mosser, and R.R.Rueckert (1993).
WIN 51711-dependent mutants of poliovirus type 3: evidence that virions decay after release from cells unless drug is present.
  J Virol, 67, 1246-1254.  
  8383239 D.A.Shepard, B.A.Heinz, and R.R.Rueckert (1993).
WIN 52035-2 inhibits both attachment and eclipse of human rhinovirus 14.
  J Virol, 67, 2245-2254.
PDB code: 1ruj
8397301 G.Diana, E.P.Jaeger, M.L.Peterson, and A.M.Treasurywala (1993).
The use of an algorithmic method for small molecule superimpositions in the design of antiviral agents.
  J Comput Aided Mol Des, 7, 325-335.  
  8383247 O.Ofori-Anyinam, R.Vrijsen, P.Kronenberger, and A.Boeyé (1993).
Effect of a capsid-stabilizing pyridazinamine, R 78206, on the eclipse and intracellular location of poliovirus.
  J Virol, 67, 2367-2369.  
1437509 E.H.Wiltink (1992).
Future prospects in antiviral therapy.
  Pharm Weekbl Sci, 14, 268-274.  
1583540 H.J.Böhm (1992).
The computer program LUDI: a new method for the de novo design of enzyme inhibitors.
  J Comput Aided Mol Des, 6, 61-78.  
1332036 V.L.Giranda, B.A.Heinz, M.A.Oliveira, I.Minor, K.H.Kim, P.R.Kolatkar, M.G.Rossmann, and R.R.Rueckert (1992).
Acid-induced structural changes in human rhinovirus 14: possible role in uncoating.
  Proc Natl Acad Sci U S A, 89, 10213-10217.  
  1850030 M.J.Almela, M.E.González, and L.Carrasco (1991).
Inhibitors of poliovirus uncoating efficiently block the early membrane permeabilization induced by virus particles.
  J Virol, 65, 2572-2577.  
  1651227 T.O.Yeates, D.H.Jacobson, A.Martin, C.Wychowski, M.Girard, D.J.Filman, and J.M.Hogle (1991).
Three-dimensional structure of a mouse-adapted type 2/type 1 poliovirus chimera.
  EMBO J, 10, 2331-2341.  
2124709 A.J.Prongay, T.J.Smith, M.G.Rossmann, L.S.Ehrlich, C.A.Carter, and J.McClure (1990).
Preparation and crystallization of a human immunodeficiency virus p24-Fab complex.
  Proc Natl Acad Sci U S A, 87, 9980-9984.  
  2152812 K.Kirkegaard (1990).
Mutations in VP1 of poliovirus specifically affect both encapsidation and release of viral RNA.
  J Virol, 64, 195-206.  
  2168152 S.R.Yasin, W.al-Nakib, and D.A.Tyrrell (1990).
Pathogenicity for humans of human rhinovirus type 2 mutants resistant to or dependent on chalcone Ro 09-0410.
  Antimicrob Agents Chemother, 34, 963-966.  
  2542566 B.A.Heinz, R.R.Rueckert, D.A.Shepard, F.J.Dutko, M.A.McKinlay, M.Fancher, M.G.Rossmann, J.Badger, and T.J.Smith (1989).
Genetic and molecular analyses of spontaneous mutants of human rhinovirus 14 that are resistant to an antiviral compound.
  J Virol, 63, 2476-2485.  
  2539499 D.C.Pevear, M.J.Fancher, P.J.Felock, M.G.Rossmann, M.S.Miller, G.Diana, A.M.Treasurywala, M.A.McKinlay, and F.J.Dutko (1989).
Conformational change in the floor of the human rhinovirus canyon blocks adsorption to HeLa cell receptors.
  J Virol, 63, 2002-2007.  
  2548847 D.J.Filman, R.Syed, M.Chow, A.J.Macadam, P.D.Minor, and J.M.Hogle (1989).
Structural factors that control conformational transitions and serotype specificity in type 3 poliovirus.
  EMBO J, 8, 1567-1579.
PDB code: 2plv
2558377 J.Badger, I.Minor, M.A.Oliveira, T.J.Smith, and M.G.Rossmann (1989).
Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses.
  Proteins, 6, 1.
PDB codes: 1r08 2r04 2r06 2r07 2rm2 2rr1 2rs1 2rs3 2rs5
2548460 K.Andries, B.Dewindt, J.Snoeks, and R.Willebrords (1989).
Lack of quantitative correlation between inhibition of replication of rhinoviruses by an antiviral drug and their stabilization.
  Arch Virol, 106, 51-61.  
  2560913 M.G.Rossmann (1989).
The canyon hypothesis.
  Viral Immunol, 2, 143-161.  
  2559655 M.G.Woods, G.D.Diana, M.C.Rogge, M.J.Otto, F.J.Dutko, and M.A.McKinlay (1989).
In vitro and in vivo activities of WIN 54954, a new broad-spectrum antipicornavirus drug.
  Antimicrob Agents Chemother, 33, 2069-2074.  
  2535737 R.J.Colonno, P.L.Callahan, D.M.Leippe, R.R.Rueckert, and J.E.Tomassini (1989).
Inhibition of rhinovirus attachment by neutralizing monoclonal antibodies and their Fab fragments.
  J Virol, 63, 36-42.  
  2773516 W.H.Prusoff, T.S.Lin, E.M.August, T.G.Wood, and M.E.Marongiu (1989).
Approaches to antiviral drug development.
  Yale J Biol Med, 62, 215-225.  
3133655 M.G.Rossmann (1988).
Antiviral agents targeted to interact with viral capsid proteins and a possible application to human immunodeficiency virus.
  Proc Natl Acad Sci U S A, 85, 4625-4627.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.