4PID | pdb_00004pid

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

• PDB DOI: https://doi.org/10.2210/pdb4PID/pdb

• Classification: Hydrolase/Hydrolase Inhibitor
• Organism(s): Human adenovirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-05-08 Released: 2014-09-10 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

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

• PubMed: 25147618 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.77 kDa 
• Atom Count: 1,918 
• Modelled Residue Count: 215 
• Deposited Residue Count: 215 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A	204	Human adenovirus 2	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pre-protein VI	B	11	Human adenovirus 2	Mutation(s): 0
UniProt
Find proteins for P03274 (Human adenovirus C serotype 2) Explore P03274  Go to UniProtKB:  P03274

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2UQ	D [auth A]	N-benzyl-2-[(Z)-iminomethyl]pyrimidine-5-carboxamide C13 H12 N4 O LOHVEJATQLMRBB-MKMNVTDBSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.783	α = 90
b = 112.783	β = 90
c = 50.347	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-10 
Deposition Author(s): 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.

Revision History  

• Version 1.0: 2014-09-10
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary