2HWC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • Primary Citation of Related Structures:  
  • Also Cited By: 1QJY, 1QJX, 1QJU

  • 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: 
    • 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
    • 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
    • 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
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP1)
1
289Human rhinovirus 14Mutation(s): 0 
Find proteins for P03303 (Human rhinovirus 14)
Go to UniProtKB:  P03303
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP2)
2
262Human rhinovirus 14Mutation(s): 0 
Find proteins for P03303 (Human rhinovirus 14)
Go to UniProtKB:  P03303
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP3)
3
236Human rhinovirus 14Mutation(s): 0 
Find proteins for P03303 (Human rhinovirus 14)
Go to UniProtKB:  P03303
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP4)
4
68Human rhinovirus 14Mutation(s): 0 
Find proteins for P03303 (Human rhinovirus 14)
Go to UniProtKB:  P03303
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
W54
Query on W54

Download SDF File 
Download CCD File 
1
5-(5-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLY)PHENOXY)PENTYL)-3-METHYL ISOXAZOLE
WIN54954
C18 H20 Cl2 N2 O3
JJDHAOLOHQTGMG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 445.100α = 90.00
b = 445.100β = 90.00
c = 445.100γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-11-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance