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PDBsum entry 1ncr

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protein ligands metals Protein-protein interface(s) links
Virus PDB id
1ncr
Jmol
Contents
Protein chains
285 a.a. *
252 a.a. *
238 a.a. *
29 a.a. *
Ligands
W11
MYR
Metals
_ZN
Waters ×338
* Residue conservation analysis
PDB id:
1ncr
Name: Virus
Title: The structure of rhinovirus 16 when complexed with pleconaril, an antiviral compound
Structure: Coat protein vp1. Chain: a. Coat protein vp2. Chain: b. Coat protein vp3. Chain: c. Coat protein vp4. Chain: d
Source: Human rhinovirus 16. Organism_taxid: 31708. Organism_taxid: 31708
Resolution:
2.70Å     R-factor:   0.243     R-free:   0.247
Authors: Y.Zhang,A.A.Simpson,C.M.Bator,S.Chakravarty,D.C.Pevear, G.A.Skochko,T.M.Tull,G.Diana,M.G.Rossmann
Key ref: Y.Zhang et al. (2004). Structural and virological studies of the stages of virus replication that are affected by antirhinovirus compounds. J Virol, 78, 11061-11069. PubMed id: 15452226
Date:
05-Dec-02     Release date:   16-Dec-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q82122  (POLG_HRV16) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2153 a.a.
285 a.a.
Protein chain
Pfam   ArchSchema ?
Q82122  (POLG_HRV16) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2153 a.a.
252 a.a.
Protein chain
Pfam   ArchSchema ?
Q82122  (POLG_HRV16) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2153 a.a.
238 a.a.
Protein chain
Pfam   ArchSchema ?
Q82122  (POLG_HRV16) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2153 a.a.
29 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: Chains A, B, C, D: E.C.2.7.7.48  - RNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Nucleoside triphosphate
+ RNA(n)
= diphosphate
+ RNA(n+1)
   Enzyme class 3: Chains A, B, C, D: E.C.3.4.22.28  - Picornain 3C.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
   Enzyme class 4: Chains A, B, C, D: E.C.3.4.22.29  - Picornain 2A.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Selective cleavage of Tyr-|-Gly bond in the picornavirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
   Enzyme class 5: Chains A, B, C, D: E.C.3.6.1.15  - Nucleoside-triphosphate phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NTP + H2O = NDP + phosphate
NTP
+ H(2)O
= NDP
+ phosphate
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     viral capsid   1 term 
  Biochemical function     structural molecule activity     1 term  

 

 
    reference    
 
 
J Virol 78:11061-11069 (2004)
PubMed id: 15452226  
 
 
Structural and virological studies of the stages of virus replication that are affected by antirhinovirus compounds.
Y.Zhang, A.A.Simpson, R.M.Ledford, C.M.Bator, S.Chakravarty, G.A.Skochko, T.M.Demenczuk, A.Watanyar, D.C.Pevear, M.G.Rossmann.
 
  ABSTRACT  
 
Pleconaril is a broad-spectrum antirhinovirus and antienterovirus compound that binds into a hydrophobic pocket within viral protein 1, stabilizing the capsid and resulting in the inhibition of cell attachment and RNA uncoating. When crystals of human rhinovirus 16 (HRV16) and HRV14 are incubated with pleconaril, drug occupancy in the binding pocket is lower than when pleconaril is introduced during assembly prior to crystallization. This effect is far more marked in HRV16 than in HRV14 and is more marked with pleconaril than with other compounds. These observations are consistent with virus yield inhibition studies and radiolabeled drug binding studies showing that the antiviral effect of pleconaril against HRV16 is greater on the infectivity of progeny virions than the parent input viruses. These data suggest that drug integration into the binding pocket during assembly, or at some other late stage in virus replication, may contribute to the antiviral activity of capsid binding compounds.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19714577 J.M.Rollinger, and M.Schmidtke (2011).
The human rhinovirus: human-pathological impact, mechanisms of antirhinoviral agents, and strategies for their discovery.
  Med Res Rev, 31, 42-92.  
18529043 A.Sun, J.J.Yoon, Y.Yin, A.Prussia, Y.Yang, J.Min, R.K.Plemper, and J.P.Snyder (2008).
Potent non-nucleoside inhibitors of the measles virus RNA-dependent RNA polymerase complex.
  J Med Chem, 51, 3731-3741.  
  19053243 Z.Zhou, M.Khaliq, J.E.Suk, C.Patkar, L.Li, R.J.Kuhn, and C.B.Post (2008).
Antiviral compounds discovered by virtual screening of small-molecule libraries against dengue virus E protein.
  ACS Chem Biol, 3, 765-775.  
17406612 A.Zlotnick, A.Lee, C.R.Bourne, J.M.Johnson, P.L.Domanico, and S.J.Stray (2007).
In vitro screening for molecules that affect virus capsid assembly (and other protein association reactions).
  Nat Protoc, 2, 490-498.  
17334823 K.H.Kim (2007).
Outliers in SAR and QSAR: is unusual binding mode a possible source of outliers?
  J Comput Aided Mol Des, 21, 63-86.  
17161425 R.B.Gonçalves, Y.S.Mendes, M.R.Soares, U.Katpally, T.J.Smith, J.L.Silva, and A.C.Oliveira (2007).
VP4 protein from human rhinovirus 14 is released by pressure and locked in the capsid by the antiviral compound WIN.
  J Mol Biol, 366, 295-306.  
16868986 Y.Y.Ke, Y.C.Chen, and T.H.Lin (2006).
Structure of the virus capsid protein VP1 of enterovirus 71 predicted by some homology modeling and molecular docking studies.
  J Comput Chem, 27, 1556-1570.  
16251287 D.C.Pevear, F.G.Hayden, T.M.Demenczuk, L.R.Barone, M.A.McKinlay, and M.S.Collett (2005).
Relationship of pleconaril susceptibility and clinical outcomes in treatment of common colds caused by rhinoviruses.
  Antimicrob Agents Chemother, 49, 4492-4499.  
15899980 Y.Li, Z.Zhou, and C.B.Post (2005).
Dissociation of an antiviral compound from the internal pocket of human rhinovirus 14 capsid.
  Proc Natl Acad Sci U S A, 102, 7529-7534.  
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.