2XYA

Non-covalent inhibtors of rhinovirus 3C protease.

PDB DOI: https://doi.org/10.2210/pdb2XYA/pdb

Classification: HYDROLASE
Organism(s): Human rhinovirus sp.
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-11-16 Released: 2011-04-27
Deposition Author(s): Petersen, J., Edman, K., Edfeldt, F., Johansson, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.288
R-Value Work: 0.227
R-Value Observed: 0.230

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Non-Covalent Inhibitors of Rhinovirus 3C Protease.

Baxter, A., Chambers, M., Edfeldt, F., Edman, K., Freeman, A., Johansson, C., King, S., Morley, A., Petersen, J., Rawlins, P., Spadola, L., Thong, B., Poel, H.V., Williams, N.

(2011) Bioorg Med Chem Lett 21: 777

PubMed: 21183345 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2010.11.110
Primary Citation of Related Structures:
2XYA

PubMed Abstract:
The first known non-covalent inhibitors of rhinovirus 3C protease (3CP) have been identified through fragment based screening and hit identification activities.

Organizational Affiliation

AstraZeneca, R&D Charnwood, Bakewell Road, Loughborough, Leicestershire LE11 5RH, UK.

Macromolecule Content

Total Structure Weight: 20.35 kDa
Atom Count: 1,462
Modelled Residue Count: 182
Deposited Residue Count: 182
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PICORNAIN 3C	A	182	Human rhinovirus sp.	Mutation(s): 0 EC: 3.4.22.28
UniProt
Find proteins for P04936 (Human rhinovirus 2) Explore P04936 Go to UniProtKB: P04936
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04936
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7L4 Query on 7L4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	2-PHENYLQUINOLIN-4-OL C₁₅ H₁₁ N O JGABMVVOXLQCKZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
7L4	Binding MOAD: 2XYA	Kd: 2.00e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.288
R-Value Work: 0.227
R-Value Observed: 0.230
Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.143	α = 90
b = 126.143	β = 90
c = 75.454	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-04-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-04-27
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.