5SQ4

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z2364980062 - (R) isomer

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.132 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Iterative computational design and crystallographic screening identifies potent inhibitors targeting 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.S., Moroz, Y.S., 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.

(2023) Proc Natl Acad Sci U S A 120: e2212931120-e2212931120

  • DOI: https://doi.org/10.1073/pnas.2212931120
  • 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, at the outset of the COVID-19 pandemic, there were no well-validated inhibitors for this protein nor, indeed, the macrodomain enzyme family, making this target a pharmacological orphan ...

    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, at the outset of the COVID-19 pandemic, there were no well-validated inhibitors for this protein nor, indeed, the macrodomain enzyme family, making this target a pharmacological orphan. Here, we report the structure-based discovery and development of several different chemical scaffolds exhibiting low- to sub-micromolar affinity for Mac1 through iterations of computer-aided design, structural characterization by ultra-high-resolution protein crystallography, and binding evaluation. Potent scaffolds were designed with in silico fragment linkage and by ultra-large library docking of over 450 million molecules. Both techniques leverage the computational exploration of tangible chemical space and are applicable to other pharmacological orphans. Overall, 160 ligands in 119 different scaffolds were discovered, and 153 Mac1-ligand complex crystal structures were determined, typically to 1 Å resolution or better. Our analyses discovered selective and cell-permeable molecules, unexpected ligand-mediated conformational changes within the active site, and key inhibitor motifs that will template future drug development against Mac1.

    Related Citations: 
    • 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 --: --
    Organizational Affiliation: 

    Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 3
A, B
169Severe 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
QKC (Subject of Investigation/LOI)
Query on QKC
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		7-fluoro-4-[(3R)-3-(methanesulfonyl)piperidin-1-yl]-9H-pyrimido[4,5-b]indole
C16 H17 F N4 O2 S
VROCEIAKWXKTQX-LLVKDONJSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.132 
  • Space Group: P 43
  • Diffraction Data: https://doi.org/10.18430/M35SQ4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.807α = 90
b = 88.807β = 90
c = 39.521γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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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: 2022-07-06
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references