4XQB

CRYSTAL STRUCTURE OF AD37 FIBER KNOB IN COMPLEX WITH TRIVALENT SIALIC ACID INHIBITOR ME0461

  • Classification: VIRAL PROTEIN
  • Organism(s): Human adenovirus D37
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2015-01-19 Released: 2015-07-29 
  • Deposition Author(s): Stehle, T., Liaci, A.M.
  • Funding Organization(s): German Research Foundation, Swedish Research Council, Knut and Alice Wallenberg Foundation, Stiftelsen foer Strategisk Forskning, Torsten Soederbergs Stiftelse

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Triazole linker-based trivalent sialic acid inhibitors of adenovirus type 37 infection of human corneal epithelial cells.

Caraballo, R.Saleeb, M.Bauer, J.Liaci, A.M.Chandra, N.Storm, R.J.Frangsmyr, L.Qian, W.Stehle, T.Arnberg, N.Elofsson, M.

(2015) Org Biomol Chem 13: 9194-9205

  • DOI: https://doi.org/10.1039/c5ob01025j
  • Primary Citation of Related Structures:  
    4K6T, 4K6U, 4K6V, 4K6W, 4XQA, 4XQB

  • PubMed Abstract: 

    Adenovirus type 37 (Ad37) is one of the principal agents responsible for epidemic keratoconjunctivitis (EKC), a severe ocular infection that remains without any available treatment. Recently, a trivalent sialic acid derivative (ME0322, Angew. Chem. Int. Ed., 2011, 50, 6519) was shown to function as a highly potent inhibitor of Ad37, efficiently preventing the attachment of the virion to the host cells and subsequent infection. Here, new trivalent sialic acid derivatives were designed, synthesized and their inhibitory properties against Ad37 infection of the human corneal epithelial cells were investigated. In comparison to ME0322, the best compound (17a) was found to be over three orders of magnitude more potent in a cell-attachment assay (IC50 = 1.4 nM) and about 140 times more potent in a cell-infection assay (IC50 = 2.9 nM). X-ray crystallographic analysis demonstrated a trivalent binding mode of all compounds to the Ad37 fiber knob. For the most potent compound ophthalmic toxicity in rabbits was investigated and it was concluded that repeated eye administration did not cause any adverse effects.


  • Organizational Affiliation

    Department of Chemistry, Umeå University, SE90187 Umeå, Sweden. mikael.elofsson@chem.umu.se.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fiber
A, B, C
194Human adenovirus D37Mutation(s): 0 
Gene Names: L5
UniProt
Find proteins for Q64823 (Human adenovirus D37)
Explore Q64823 
Go to UniProtKB:  Q64823
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ64823
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
425
Query on 425

Download Ideal Coordinates CCD File 
D [auth A]2-(1-{2-[bis(2-{4-[2-({(6R)-5-(acetylamino)-3,5-dideoxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]-beta-L-threo-hex-2-ulopyranonosyl}oxy)ethyl]-1H-1,2,3-triazol-1-yl}ethyl)amino]ethyl}-1H-1,2,3-triazol-4-yl)ethyl (6R)-5-(acetylamino)-3,5-dideoxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]-beta-L-threo-hex-2-ulopyranosidonic acid
C51 H81 N13 O27
BLJKNJLUKOGWGY-UYSYNVRDSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
H [auth A],
L [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
G [auth A]
I [auth A]
J [auth A]
K [auth A]
M [auth B]
G [auth A],
I [auth A],
J [auth A],
K [auth A],
M [auth B],
N [auth B],
O [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
425 Binding MOAD:  4XQB Kd: 1.63e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.44α = 90
b = 70.32β = 94.47
c = 74.48γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB 685
Swedish Research CouncilSweden521-2010-3078
Swedish Research CouncilSweden621-2010-4746
Knut and Alice Wallenberg FoundationSweden2009.0009
Stiftelsen foer Strategisk ForskningSwedenF06-0011
Torsten Soederbergs StiftelseSwedenM4/11

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2015-09-02
    Changes: Database references
  • Version 2.0: 2017-09-06
    Changes: Advisory, Atomic model, Author supporting evidence, Derived calculations
  • Version 2.1: 2019-06-12
    Changes: Data collection, Structure summary
  • Version 2.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description