RCSB PDB - 4PIS: Crystal structure of human adenovirus 8 protease in complex with a nitrile inhibitor

 4PIS

Crystal structure of human adenovirus 8 protease in complex with a nitrile inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.3 of the entry. See complete history


Literature

Discovery and structure-based optimization of adenain inhibitors.

Mac Sweeney, A.Grosche, P.Ellis, D.Combrink, K.Erbel, P.Hughes, N.Sirockin, F.Melkko, S.Bernardi, A.Ramage, P.Jarousse, N.Altmann, E.

(2014) ACS Med Chem Lett 5: 937-941

  • DOI: https://doi.org/10.1021/ml500224t
  • Primary Citation of Related Structures:  
    4PID, 4PIE, 4PIQ, 4PIS

  • PubMed Abstract: 

    The cysteine protease adenain is the essential protease of adenovirus and, as such, represents a promising target for the treatment of ocular and other adenoviral infections. Through a concise two-pronged hit discovery approach we identified tetrapeptide nitrile 1 and pyrimidine nitrile 2 as complementary starting points for adenain inhibition. These hits enabled the first high-resolution X-ray cocrystal structures of adenain with inhibitors bound and revealed the binding mode of 1 and 2. The screening hits were optimized by a structure-guided medicinal chemistry strategy into low nanomolar drug-like inhibitors of adenain.


  • Organizational Affiliation

    Novartis Institute for Biomedical Research , Novartis Campus, CH-4002 Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protease204Human adenovirus D8Mutation(s): 0 
Gene Names: L3
EC: 3.4.22.39
UniProt
Find proteins for B9A5C1 (Human adenovirus D serotype 8)
Explore B9A5C1 
Go to UniProtKB:  B9A5C1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9A5C1
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PVI11Human adenovirus D8Mutation(s): 0 
UniProt
Find proteins for B9A5B9 (Human adenovirus D serotype 8)
Explore B9A5B9 
Go to UniProtKB:  B9A5B9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9A5B9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3FU
Query on 3FU

Download Ideal Coordinates CCD File 
C [auth A]N~2~-[(2R)-2-(3,5-dichlorophenyl)-2-(dimethylamino)acetyl]-N-({2-[(Z)-iminomethyl]pyrimidin-4-yl}methyl)-L-isoleucinamide
C22 H28 Cl2 N6 O2
XBUAFLLXSYLZPV-GKZFGAONSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.061α = 90
b = 42.061β = 90
c = 193.238γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
XSCALEdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3FUClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2017-08-23
    Changes: Data collection, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-30
    Changes: Structure summary