4PIE | pdb_00004pie

Crystal structure of human adenovirus 2 protease a substrate based nitrile inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 
    0.260 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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

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 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03252
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-protein VI11Human adenovirus 2Mutation(s): 0 
UniProt
Find proteins for P03274 (Human adenovirus C serotype 2)
Explore P03274 
Go to UniProtKB:  P03274
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03274
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3FO
Query on 3FO

Download Ideal Coordinates CCD File 
C [auth A]N-{(2S)-2-(3-chlorophenyl)-2-[(methylsulfonyl)amino]acetyl}-L-phenylalanyl-N-[(2Z)-2-iminoethyl]glycinamide
C22 H26 Cl N5 O5 S
RAJSHKUFRQXBIW-SUWYLCKESA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free:  0.260 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.312α = 90
b = 44.437β = 90
c = 98.921γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling

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 3FOClick 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: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary