3VDD | pdb_00003vdd

Structure of HRV2 capsid complexed with antiviral compound BTA798

PDB DOI: https://doi.org/10.2210/pdb3VDD/pdb

Classification: VIRUS
Organism(s): rhinovirus A2
Mutation(s): No

Deposited: 2012-01-05 Released: 2012-09-12
Deposition Author(s): Morton, C.J., Feil, S.C., Parker, M.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.273 (Depositor), 0.291 (DCC)
R-Value Work:
0.230 (Depositor), 0.287 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

An Orally Available 3-Ethoxybenzisoxazole Capsid Binder with Clinical Activity against Human Rhinovirus.

Feil, S.C., Hamilton, S., Krippner, G.Y., Lin, B., Luttick, A., McConnell, D.B., Nearn, R., Parker, M.W., Ryan, J., Stanislawski, P.C., Tucker, S.P., Watson, K.G., Morton, C.J.

(2012) ACS Med Chem Lett 3: 303-307

PubMed: 24900468 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/ml2002955
Primary Citation Related Structures:
3VDD

PubMed Abstract:
Respiratory infections caused by human rhinovirus are responsible for severe exacerbations of underlying clinical conditions such as asthma in addition to their economic cost in terms of lost working days due to illness. While several antiviral compounds for treating rhinoviral infections have been discovered, none have succeeded, to date, in reaching approval for clinical use. We have developed a potent, orally available rhinovirus inhibitor 6 that has progressed through early clinical trials. The compound shows favorable pharmacokinetic and activity profiles and has a confirmed mechanism of action through crystallographic studies of a rhinovirus-compound complex. The compound has now progressed to phase IIb clinical studies of its effect on natural rhinovirus infection in humans.

Organizational Affiliation

Biota Structural Biology Laboratory, St. Vincent's Institute , 9 Princes Street, Fitzroy, Victoria 3065, Australia.

Macromolecule Content

Total Structure Weight: 95.26 kDa
Atom Count: 6,380
Modeled Residue Count: 804
Deposited Residue Count: 850
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein VP1	A	283	rhinovirus A2	Mutation(s): 0
UniProt
Find proteins for P04936 (Human rhinovirus 2) Explore P04936 Go to UniProtKB: P04936
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04936
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein VP2	B	261	rhinovirus A2	Mutation(s): 0
UniProt
Find proteins for P04936 (Human rhinovirus 2) Explore P04936 Go to UniProtKB: P04936
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04936
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein VP3	C	237	rhinovirus A2	Mutation(s): 0
UniProt
Find proteins for P04936 (Human rhinovirus 2) Explore P04936 Go to UniProtKB: P04936
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04936
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein VP4	D	69	rhinovirus A2	Mutation(s): 0
UniProt
Find proteins for P04936 (Human rhinovirus 2) Explore P04936 Go to UniProtKB: P04936
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04936
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BT8 Query on BT8 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	3-ethoxy-6-{2-[1-(6-methylpyridazin-3-yl)piperidin-4-yl]ethoxy}-1,2-benzoxazole C₂₁ H₂₆ N₄ O₃ DKSVBVKHUICELN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.273 (Depositor), 0.291 (DCC)
R-Value Work: 0.230 (Depositor), 0.287 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 310.49	α = 90
b = 345.68	β = 90
c = 378.39	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-09-12

Deposition Author(s):

Morton, C.J.

Feil, S.C.

Parker, M.W.

Revision History (Full details and data files)

Version 1.0: 2012-09-12
Type: Initial release
Version 1.1: 2014-09-24
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description