Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 34.87 kDa 
• Atom Count: 2617 
• Residue Count: 306 
• Unique protein chains: 1

7JYC

Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) in Complex with Covalent Inhibitor Narlaprevir

• DOI: 10.2210/pdb7JYC/pdb

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


• Deposited: 2020-08-30 Released: 2020-09-09 
• Deposition Author(s): Andi, B., Kumaran, D., Kreitler, D.F., Soares, A.S., Shi, W., Jakoncic, J., Fuchs, M.R., Keereetaweep, J., Shanklin, J., McSweeney, S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States), Brookhaven National Laboratory (BNL), National Virtual Biotechnology Laboratory (NVBL)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.212 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

Literature

Hepatitis C Virus NSP3/NSP4A Inhibitors as Promising Lead Compounds for the Design of New Covalent Inhibitors for SARS-CoV-2 3CLpro/Mpro Protease

Andi, B., Kumaran, D., Kreitler, D.F., Soares, A.S., Shi, W., Jakoncic, J., Fuchs, M.R., Keereetaweep, J., Shanklin, J., McSweeney, S.

To be published.

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 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NNA	A	(1R,2S,5S)-3-[N-({1-[(tert-butylsulfonyl)methyl]cyclohexyl}carbamoyl)-3-methyl-L-valyl]-N-{(1S)-1-[(1R)-2-(cyclopropyla mino)-1-hydroxy-2-oxoethyl]pentyl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide C36 H63 N5 O7 S BZXRATSZUNDEEV-FZFXNXQRSA-N
DMS	A	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.212 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.188	α = 90
b = 52.507	β = 102.71
c = 45.693	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-08-30 
• Released Date: 2020-09-09 
Deposition Author(s): Andi, B., Kumaran, D., Kreitler, D.F., Soares, A.S., Shi, W., Jakoncic, J., Fuchs, M.R., Keereetaweep, J., Shanklin, J., McSweeney, S.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM133893
Department of Energy (DOE, United States)	United States	KP1605010
Brookhaven National Laboratory (BNL)	United States	LDRD 20-042
National Virtual Biotechnology Laboratory (NVBL)	United States	Coronavirus CARES Act

Revision History 

• Version 1.0: 2020-09-09
  Type: Initial release