8CZU

Structure of MERS 3CL protease in complex with the cyclopropane based inhibitor 16d


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure of MERS 3CL protease in complex with the cyclopropane based inhibitor 16d

Chamandi, S.D.Nguyen, H.N.Rathnayake, A.D.Kim, Y.Perera, K.D.Picard, H.R.Madden, T.Thurman, H.A.Kashipathy, M.M.Liu, L.Battaile, K.P.Lovell, S.Chang, K.O.Groutas, W.C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3C-like proteinaseA313Middle East respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: orf1a
EC: 3.4.19.12 (UniProt), 3.4.22.69 (UniProt)
UniProt
Find proteins for A0A1L2E0X0 (Middle East respiratory syndrome-related coronavirus)
Explore A0A1L2E0X0 
Go to UniProtKB:  A0A1L2E0X0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1L2E0X0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P9R (Subject of Investigation/LOI)
Query on P9R

Download Ideal Coordinates CCD File 
B [auth A][(1~{S},2~{S})-2-(cyclohexylmethyl)cyclopropyl]methyl ~{N}-[(2~{S})-1-[[(2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{R})-2-oxidanylidene-3,4-dihydropyrrol-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate
C25 H42 N3 O8 S
UNYDBHQZGVQZAY-KAXVZBFOSA-P
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.443α = 90
b = 57.312β = 112.21
c = 49.682γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI130092
National Institutes of Health/Office of the DirectorUnited StatesS10OD030394

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release
  • Version 1.1: 2022-08-03
    Changes: Author supporting evidence, Database references, Structure summary