7JST | pdb_00007jst

Crystal structure of SARS-CoV-2 3CL in apo form

• PDB DOI: https://doi.org/10.2210/pdb7JST/pdb

• Classification: VIRAL PROTEIN, HYDROLASE
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-08-16 Released: 2021-03-03 
• Deposition Author(s): Iketani, S., Forouhar, F., Liu, H., Hong, S.J., Lin, F.-Y., Nair, M.S., Zask, A., Huang, Y., Xing, L., Stockwell, B.R., Chavez, A., Ho, D.D.
• Funding Organization(s): Jack Ma Foundation, Columbia Technology Ventures and the Columbia Translational Therapeutics (TRx) program, Burroughs Wellcome Fund, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Center for Research Resources (NIH/NCRR), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.196 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Lead compounds for the development of SARS-CoV-2 3CL protease inhibitors.

Iketani, S., Forouhar, F., Liu, H., Hong, S.J., Lin, F.Y., Nair, M.S., Zask, A., Huang, Y., Xing, L., Stockwell, B.R., Chavez, A., Ho, D.D.

(2021) Nat Commun 12: 2016-2016

• PubMed: 33795671 
• DOI: https://doi.org/10.1038/s41467-021-22362-2
• Primary Citation Related Structures: 
  7JST, 7JSU, 7JT0, 7JT7, 7JW8


• PubMed Abstract: 
  

  We report the identification of three structurally diverse compounds - compound 4, GC376, and MAC-5576 - as inhibitors of the SARS-CoV-2 3CL protease. Structures of each of these compounds in complex with the protease revealed strategies for further development, as well as general principles for designing SARS-CoV-2 3CL protease inhibitors. These compounds may therefore serve as leads for the basis of building effective SARS-CoV-2 3CL protease inhibitors.

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Organizational Affiliation: 
• Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, USA.
Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA.
Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
Department of Chemistry, Columbia University, New York, NY, USA.
Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA.
WuXi AppTec, Cambridge, MA, USA.
Department of Biological Sciences, Columbia University, New York, NY, USA.
Department of Chemistry, Columbia University, New York, NY, USA. [e-mail].
Department of Biological Sciences, Columbia University, New York, NY, USA. [e-mail].
Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA. [e-mail].
Aaron Diamond AIDS Research Center, Columbia University Irving Medical Center, New York, NY, USA. [e-mail].
Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.92 kDa 
• Atom Count: 2,487 
• Modeled Residue Count: 301 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.196 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.659	α = 90
b = 81.982	β = 114.95
c = 51.801	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-03-03 
Deposition Author(s): Iketani, S., Forouhar, F., Liu, H., Hong, S.J., Lin, F.-Y., Nair, M.S., Zask, A., Huang, Y., Xing, L., Stockwell, B.R., Chavez, A., Ho, D.D.

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Funding Organization	Location	Grant Number
Jack Ma Foundation	China	--
Columbia Technology Ventures and the Columbia Translational Therapeutics (TRx) program	United States	--
Burroughs Wellcome Fund	United States	--
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	T32AI106711
National Science Foundation (NSF, United States)	United States	2029943
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM124165
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	RR029205
National Institutes of Health/Office of the Director	United States	OD021527

Revision History  

• Version 1.0: 2021-03-03
  Type: Initial release
  
• Version 1.1: 2021-03-10
  Changes: Structure summary
• Version 1.2: 2021-03-24
  Changes: Structure summary
• Version 1.3: 2021-04-14
  Changes: Database references
• Version 1.4: 2023-10-18
  Changes: Data collection, Database references, Refinement description