4PID

Crystal structure of human adenovirus 2 protease with a weak pyrimidine nitrile inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 10.1021/ml500224t
  • Primary Citation of Related Structures:  
    4PIE, 4PID, 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ProteaseA204Human adenovirus 2Mutation(s): 0 
Gene Names: L3
EC: 3.4.22.39
UniProt
Find proteins for P03252 (Human adenovirus C serotype 2)
Explore P03252 
Go to UniProtKB:  P03252
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-protein VIB11Human adenovirus 2Mutation(s): 0 
Gene Names: L3
UniProt
Find proteins for P03274 (Human adenovirus C serotype 2)
Explore P03274 
Go to UniProtKB:  P03274
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2UQ
Query on 2UQ

Download Ideal Coordinates CCD File 
D [auth A]N-benzyl-2-[(Z)-iminomethyl]pyrimidine-5-carboxamide
C13 H12 N4 O
LOHVEJATQLMRBB-MKMNVTDBSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.783α = 90
b = 112.783β = 90
c = 50.347γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Derived calculations, Other, Refinement description, Source and taxonomy