2HWD

A COMPARISON OF THE ANTI-RHINOVIRAL DRUG BINDING POCKET IN HRV14 AND HRV1A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A comparison of the anti-rhinoviral drug binding pocket in HRV14 and HRV1A.

Kim, K.H.Willingmann, P.Gong, Z.X.Kremer, M.J.Chapman, M.S.Minor, I.Oliveira, M.A.Rossmann, M.G.Andries, K.Diana, G.D.Dutko, F.J.McKinlay, M.A.Pevear, D.C.

(1993) J Mol Biol 230: 206-227

  • DOI: 10.1006/jmbi.1993.1137
  • Primary Citation of Related Structures:  
    2HWF, 2HWE, 2HWD, 2HWC, 2HWB

  • PubMed Abstract: 
  • The three-dimensional structures of two human rhinovirus serotypes (HRV14 and HRV1A) are compared when complexed with various antiviral agents. Although these agents all bind into the same hydrophobic pocket, the exact viral-drug interactions differ. ...

    The three-dimensional structures of two human rhinovirus serotypes (HRV14 and HRV1A) are compared when complexed with various antiviral agents. Although these agents all bind into the same hydrophobic pocket, the exact viral-drug interactions differ. In the absence of drugs, the pocket is occupied by a fatty acid in HRV1A, but is empty in HRV14 except for two water molecules. The conformation of each drug is dependent upon the shape of the hydrophobic pocket. In HRV14 the major residues determining the shape of the binding site are Y1128, P1174 and M1224, corresponding to I1125, M1169 and I1220 in HRV1A. When there is no cofactor or a drug in the pocket, the entrance to the pocket is open. However, the entrance is closed when the pocket is occupied by a cofactor or a drug. There are relatively small conformational changes when the agents displace the natural cofactor in HRV1A. In contrast, there are much larger conformational changes on binding a drug in HRV14. These differences cause an inhibition of viral attachment in HRV14 but not in HRV1A. Binding of the drugs results in three additional interprotomer hydrogen bonds in HRV14 and one in HRV1A. These hydrogen bonds and a potential loss of flexibility upon efficient packing of the pocket may contribute to the inhibition of uncoating in both serotypes.


    Related Citations: 
    • Human Rhinovirus 14 Complexed with Antiviral Compound R 61837
      Chapman, M.S., Minor, I., Rossmann, M.G., Diana, G.D., Andries, K.
      (1991) J Mol Biol 217: 455
    • Crystal Structure of Human Rhinovirus Serotype 1A (Hrv1A)
      Kim, S., Smith, T.J., Chapman, M.S., Rossmann, M.G., Pevear, D.C., Dutko, F.J., Felock, P.J., Diana, G.D., Mckinlay, M.A.
      (1989) J Mol Biol 210: 91
    • Structural Analysis of a Series of Antiviral Agents Complexed with Human Rhinovirus 14
      Badger, J., Minor, I., Kremer, M.J., Oliveira, M.A., Smith, T.J., Griffith, J.P., Guerin, D.M.A., Krishnaswamy, S., Luo, M., Rossmann, M.G., Mckinlay, M.A., Diana, G.D., Dutko, F.J., Fancher, M., Rueckert, R.R., Heinz, B.A.
      (1988) Biochemistry 85: 3304
    • The Site of Attachment in Human Rhinovirus 14 for Antiviral Agents that Inhibit Uncoating
      Smith, T.J., Kremer, M.J., Luo, M., Vriend, G., Arnold, E., Kamer, G., Rossmann, M.G., Mckinlay, M.A., Diana, G.D., Otto, M.J.
      (1986) Science 233: 1286
    • Structure of a Human Common Cold Virus and Functional Relationship to Other Picornaviruses
      Rossmann, M.G., Arnold, E., Erickson, J.W., Frankenberger, E.A., Griffith, J.P., Hecht, H.-J., Johnson, J.E., Kamer, G., Luo, M., Mosser, A.G., Rueckert, R.R., Sherry, B., Vriend, G.
      (1985) Nature 317: 145

    Organizational Affiliation

    Department of Biological Sciences, Purdue University West Lafayette, IN 47907.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP1)1287Human rhinovirus 1AMutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P23008 (Human rhinovirus 1A)
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Go to UniProtKB:  P23008
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP2)2263Human rhinovirus 1AMutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P23008 (Human rhinovirus 1A)
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP3)3238Human rhinovirus 1AMutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P23008 (Human rhinovirus 1A)
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP4)444Human rhinovirus 1AMutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P23008 (Human rhinovirus 1A)
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
W91
Query on W91

Download CCD File 
1
5-(3-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PROPYL)-3-METHYL ISOXAZOLE
C16 H16 Cl2 N2 O3
TUGBWRGTMLOFAX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 341.3α = 90
b = 341.3β = 90
c = 465.9γ = 120

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-09-30
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-03-07
    Changes: Source and taxonomy