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PDBsum entry 1hrv

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protein ligands Protein-protein interface(s) links
Virus PDB id
1hrv
Jmol
Contents
Protein chains
273 a.a. *
255 a.a. *
236 a.a. *
40 a.a. *
Ligands
SDZ
* Residue conservation analysis
PDB id:
1hrv
Name: Virus
Title: Hrv14/sdz 35-682 complex
Structure: Human rhinovirus 14 coat protein (subunit vp1). Chain: 1. Engineered: yes. Human rhinovirus 14 coat protein (subunit vp2). Chain: 2. Engineered: yes. Human rhinovirus 14 coat protein (subunit vp3). Chain: 3. Engineered: yes.
Source: Human rhinovirus 14. Organism_taxid: 12131. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: hela cells. Expression_system_cell_line: hela cells
Resolution:
3.00Å     R-factor:   not given    
Authors: D.A.Oren,A.Zhang,E.Arnold
Key ref: B.Rosenwirth et al. (1995). SDZ 35-682, a new picornavirus capsid-binding agent with potent antiviral activity. Antiviral Res, 26, 65-82. PubMed id: 7741522 DOI: 10.1016/0166-3542(94)00066-H
Date:
02-Mar-95     Release date:   03-Jun-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P03303  (POLG_HRV14) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2179 a.a.
273 a.a.
Protein chain
Pfam   ArchSchema ?
P03303  (POLG_HRV14) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2179 a.a.
255 a.a.*
Protein chain
Pfam   ArchSchema ?
P03303  (POLG_HRV14) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2179 a.a.
236 a.a.
Protein chain
Pfam   ArchSchema ?
P03303  (POLG_HRV14) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2179 a.a.
40 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 2: Chains 1, 2, 3, 4: 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 1, 2, 3, 4: 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 1, 2, 3, 4: 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 1, 2, 3, 4: 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    
 
 
DOI no: 10.1016/0166-3542(94)00066-H Antiviral Res 26:65-82 (1995)
PubMed id: 7741522  
 
 
SDZ 35-682, a new picornavirus capsid-binding agent with potent antiviral activity.
B.Rosenwirth, D.A.Oren, E.Arnold, Z.L.Kis, H.J.Eggers.
 
  ABSTRACT  
 
SDZ 35-682 is a potent and selective inhibitor of the replication of members of the picornavirus group. It inhibits several rhinovirus serotypes and echovirus 9 at concentrations as low as 0.1 micrograms/ml, without exerting any effect on cell proliferation up to 30 micrograms/ml. As observed with other capsid-binding antipicornavirus compounds, there is a wide variation in sensitivity of the different serotypes within the rhinovirus group. The point of interference of SDZ 35-682 in a single cycle of virus growth is an early event taking place before 2 or 3 h of echo- or rhinovirus replication, respectively. By incorporation of neutral red into the viral capsid and measurement of acquisition of photoresistance it is shown that uncoating of echovirus 9 is inhibited by SDZ 35-682. In addition, efficiency of adsorption of echovirus 9 is reduced by SDZ 35-682. To demonstrate that SDZ 35-682, like other uncoating inhibitors of picornaviruses, binds to the hydrophobic pocket beneath the canyon floor co-crystallization with HRV 14 was performed. Considerable conformational changes occur in VP1 in the HRV 14/SDZ 35-682 complex. SDZ 35-682 is 19 A long from end to end and thus fills the entire hydrophobic pocket including its innermost end; it is less flexible than other long antiviral agents. It has been suggested that compounds filling the entire hydrophobic pocket will affect the uncoating process of the virion. Thus, inhibition of viral uncoating, as demonstrated with echovirus 9, probably is the predominant mode of action of SDZ 35-682.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
10771083 A.Garozzo, C.C.Cutrì, A.Castro, G.Tempera, F.Guerrera, M.C.Sarvà, and E.Geremia (2000).
Anti-rhinovirus activity of 3-methylthio-5-aryl-4-isothiazolecarbonitrile derivatives.
  Antiviral Res, 45, 199-210.  
10627492 P.Leyssen, E.De Clercq, and J.Neyts (2000).
Perspectives for the treatment of infections with Flaviviridae.
  Clin Microbiol Rev, 13, 67.  
10669262 M.A.Murray, and L.M.Babe (1999).
Inhibitory effect of dibenzofuran and dibenzosuberol derivatives on rhinovirus replication in vitro; effective prevention of viral entry by dibenzosuberenone.
  Antiviral Res, 44, 123-131.  
9497072 A.Heim, U.Pfetzing, G.Müller, and I.M.Grumbach (1998).
Antiviral activity of WIN 54954 in coxsackievirus B2 carrier state infected human myocardial fibroblasts.
  Antiviral Res, 37, 47-56.  
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.