2HWE

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

DOI: 10.2210/pdb2HWE/pdb

Classification: VIRUS
Organism(s): Human rhinovirus 1A
Expression System: Homo sapiens
Mutation(s): No

Deposited: 1994-01-25 Released: 1994-09-30
Deposition Author(s): Kim, K.H., Rossmann, M.G.

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

PubMed: 8383771 Search on PubMed
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. 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
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP1)	1	287	Human rhinovirus 1A	Mutation(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) Explore P23008 Go to UniProtKB: P23008
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP2)	2	263	Human rhinovirus 1A	Mutation(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) Explore P23008 Go to UniProtKB: P23008
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP3)	3	238	Human rhinovirus 1A	Mutation(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) Explore P23008 Go to UniProtKB: P23008
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP4)	4	44	Human rhinovirus 1A	Mutation(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) Explore P23008 Go to UniProtKB: P23008
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
W54 Query on W54 Download Ideal Coordinates CCD File SDF format, chain E [1] MOL2 format, chain E [1]	1	5-(5-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLY)PHENOXY)PENTYL)-3-METHYL ISOXAZOLE C₁₈ H₂₀ Cl₂ N₂ O₃ JJDHAOLOHQTGMG-UHFFFAOYSA-N		Ligand Interaction