2HWF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 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

  • 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: 
    • 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
    • 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


    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 1A COAT PROTEIN (SUBUNIT VP1)
1
287Human rhinovirus 1AMutation(s): 0 
Find proteins for P23008 (Human rhinovirus 1A)
Go to UniProtKB:  P23008
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP2)
2
263Human rhinovirus 1AMutation(s): 0 
Find proteins for P23008 (Human rhinovirus 1A)
Go to UniProtKB:  P23008
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP3)
3
238Human rhinovirus 1AMutation(s): 0 
Find proteins for P23008 (Human rhinovirus 1A)
Go to UniProtKB:  P23008
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP4)
4
44Human rhinovirus 1AMutation(s): 0 
Find proteins for P23008 (Human rhinovirus 1A)
Go to UniProtKB:  P23008
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JEN
Query on JEN

Download SDF File 
Download CCD File 
1
3-METHOXY-6-[4-(3-METHYLPHENYL)-1-PIPERAZINYL]PYRIDAZINE
C16 H20 N4 O
DDOAUTHWSCUHQA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 341.300α = 90.00
b = 341.300β = 90.00
c = 465.900γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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