4MDS

Discovery of N-(benzo[1,2,3]triazol-1-yl)-N-(benzyl)acetamido)phenyl) carboxamides as severe acute respiratory syndrome coronavirus (SARS-CoV) 3CLpro inhibitors: identification of ML300 and non-covalent nanomolar inhibitors with an induced-fit binding


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.598 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of N-(benzo[1,2,3]triazol-1-yl)-N-(benzyl)acetamido)phenyl) carboxamides as severe acute respiratory syndrome coronavirus (SARS-CoV) 3CLpro inhibitors: Identification of ML300 and noncovalent nanomolar inhibitors with an induced-fit binding.

Turlington, M.Chun, A.Tomar, S.Eggler, A.Grum-Tokars, V.Jacobs, J.Daniels, J.S.Dawson, E.Saldanha, A.Chase, P.Baez-Santos, Y.M.Lindsley, C.W.Hodder, P.Mesecar, A.D.Stauffer, S.R.

(2013) Bioorg.Med.Chem.Lett. 23: 6172-6177

  • DOI: 10.1016/j.bmcl.2013.08.112

  • PubMed Abstract: 
  • Herein we report the discovery and SAR of a novel series of SARS-CoV 3CLpro inhibitors identified through the NIH Molecular Libraries Probe Production Centers Network (MLPCN). In addition to ML188, ML300 represents the second probe declared for 3CLpr ...

    Herein we report the discovery and SAR of a novel series of SARS-CoV 3CLpro inhibitors identified through the NIH Molecular Libraries Probe Production Centers Network (MLPCN). In addition to ML188, ML300 represents the second probe declared for 3CLpro from this collaborative effort. The X-ray structure of SARS-CoV 3CLpro bound with a ML300 analog highlights a unique induced-fit reorganization of the S2-S4 binding pockets leading to the first sub-micromolar noncovalent 3CLpro inhibitors retaining a single amide bond.


    Organizational Affiliation

    Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Specialized Chemistry Center for Probe Development (MLPCN), Nashville, TN 37232, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3C-like proteinase
A
303Human SARS coronavirusMutation(s): 0 
Find proteins for P0C6U8 (Human SARS coronavirus)
Go to UniProtKB:  P0C6U8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
23H
Query on 23H

Download SDF File 
Download CCD File 
A
N-[4-(acetylamino)phenyl]-2-(1H-benzotriazol-1-yl)-N-[(1R)-2-[(2-methylbutan-2-yl)amino]-1-(1-methyl-1H-pyrrol-2-yl)-2-oxoethyl]acetamide
C28 H33 N7 O3
BCIIGGMNYNWRQK-AREMUKBSSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
23HIC50: 6200 nM BINDINGMOAD
23HIC50: 6200 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.598 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.170 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 118.824α = 90.00
b = 56.244β = 111.13
c = 53.140γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
MOLREPphasing
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-10-16
    Type: Database references
  • Version 1.2: 2013-11-06
    Type: Database references