5SOJ

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000642067873 - (R) isomer

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.135 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.

Gahbauer, S., Correy, G.J., Schuller, M., Ferla, M.P., Doruk, Y.U., Rachman, M., Wu, T., Diolaiti, M., Wang, S., Neitz, R.J., Fearon, D., Radchenko, D., Moroz, Y., Irwin, J.J., Renslo, A.R., Taylor, J.C., Gestwicki, J.E., von Delft, F., Ashworth, A., Ahel, I., Shoichet, B.K., Fraser, J.S.

(2022) Biorxiv 

  • DOI: https://doi.org/10.1101/2022.06.27.497816
  • Primary Citation of Related Structures:  
    5SOI, 5SOJ, 5SOK, 5SOL, 5SOM, 5SON, 5SOO, 5SOP, 5SOQ, 5SOR, 5SOS, 5SOT, 5SOU, 5SOV, 5SOW, 5SOX, 5SOY, 5SOZ, 5SP0, 5SP1, 5SP2, 5SP3, 5SP4, 5SP6, 5SP7, 5SP8, 5SP9, 5SPA, 5SPB, 5SPC, 5SPD, 5SPE, 5SPF, 5SPG, 5SPH, 5SPI, 5SPJ, 5SPK, 5SPL, 5SPM, 5SPN, 5SPO, 5SPP, 5SPQ, 5SPR, 5SPS, 5SPT, 5SPU, 5SPV, 5SPW

  • PubMed Abstract: 

    • The nonstructural protein 3 (NSP3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contains a conserved macrodomain enzyme (Mac1) that is critical for pathogenesis and lethality. While small molecule inhibitors of Mac1 have great therapeutic potential, few have been described ...

    The nonstructural protein 3 (NSP3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contains a conserved macrodomain enzyme (Mac1) that is critical for pathogenesis and lethality. While small molecule inhibitors of Mac1 have great therapeutic potential, few have been described. Here, we report the structure-based development of several chemical scaffolds exhibiting low- to sub-micromolar affinity for Mac1 through iterations of computer-aided design, structural characterization by ultra-high resolution X-ray protein crystallography, and binding evaluation with in-solution assays. Potent scaffolds were designed with in silico linkage of previously obtained fragment hits and ultra-large library docking screens of more than 450 million molecules. In total, 160 hits comprising 119 different scaffolds were discovered and 152 Mac1-ligand complex crystal structures were determined, typically to 1 Ã… resolution or better. The structure-activity-relationships emerging from this study may template future drug development against Mac1.

    Organizational Affiliation: 

    Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. mamzel@jhmi.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 3A, B169Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep, 1a-1b
EC: 3.4.22 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RWQ (Subject of Investigation/LOI)
Query on RWQ
Download Ideal Coordinates CCD File 
C [auth A][(3R)-1-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)piperidin-3-yl]methanol
C16 H17 F N4 O
LEHSMGCFXRLFLE-SNVBAGLBSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.135 
  • Space Group: P 43
  • Diffraction Data: https://doi.org/10.18430/M35SOJ
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.881α = 90
b = 88.881β = 90
c = 39.637γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States2031205

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references