6LZE

The crystal structure of COVID-19 main protease in complex with an inhibitor 11a

• PDB DOI:  https://doi.org/10.2210/pdb6LZE/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-02-19 Released: 2020-04-29 
• Deposition Author(s): Zhang, B., Zhang, Y., Jing, Z., Liu, X., Yang, H., Liu, H., Rao, Z., Jiang, H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Chinese Academy of Sciences

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.199 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 

Literature

Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease.

Dai, W., Zhang, B., Jiang, X.M., Su, H., Li, J., Zhao, Y., Xie, X., Jin, Z., Peng, J., Liu, F., Li, C., Li, Y., Bai, F., Wang, H., Cheng, X., Cen, X., Hu, S., Yang, X., Wang, J., Liu, X., Xiao, G., Jiang, H., Rao, Z., Zhang, L.K., Xu, Y., Yang, H., Liu, H.

(2020) Science 368: 1331-1335

• PubMed: 32321856 
• DOI: https://doi.org/10.1126/science.abb4489
• Primary Citation of Related Structures:  
  6LZE, 6M0K


• PubMed Abstract: 
  

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is the etiological agent responsible for the global COVID-19 (coronavirus disease 2019) outbreak. The main protease of SARS-CoV-2, M ^pro , is a key enzyme that plays a pivotal role in mediating viral replication and transcription. We designed and synthesized two lead compounds ( 11a and 11b ) targeting M ^pro Both exhibited excellent inhibitory activity and potent anti-SARS-CoV-2 infection activity. The x-ray crystal structures of SARS-CoV-2 M ^pro in complex with 11a or 11b , both determined at a resolution of 1.5 angstroms, showed that the aldehyde groups of 11a and 11b are covalently bound to cysteine 145 of M ^pro Both compounds showed good pharmacokinetic properties in vivo, and 11a also exhibited low toxicity, which suggests that these compounds are promising drug candidates.

---

Organizational Affiliation: 

College of Pharmacy, Nanjing University of Chinese Medicine, Qixia District, Nanjing 210023, China.

Biological Assembly 1  

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

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

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content

• Total Structure Weight: 34.21 kDa 
• Atom Count: 2,598 
• Modelled Residue Count: 303 
• Deposited Residue Count: 303 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	303	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), 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FHR	F [auth A]	~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide C25 H32 N4 O4 HPKJGHVHQWJOOT-ZJOUEHCJSA-N
DMS	B [auth A], C [auth A], D [auth A], E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002347 (FHR)	F [auth A]	~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide	Peptide-like / Inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.199 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.696	α = 90
b = 80.938	β = 114.27
c = 51.738	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-04-29 
Deposition Author(s): Zhang, B., Zhang, Y., Jing, Z., Liu, X., Yang, H., Liu, H., Rao, Z., Jiang, H.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81520108019
Chinese Academy of Sciences	China	2017YFC0840300

Revision History  

• Version 1.0: 2020-04-29
  Type: Initial release
  
• Version 1.1: 2020-05-06
  Changes: Database references, Source and taxonomy, Structure summary
• Version 2.0: 2020-05-27
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2020-06-03
  Changes: Structure summary
• Version 2.2: 2020-06-10
  Changes: Structure summary
• Version 2.3: 2020-07-01
  Changes: Database references
• Version 2.4: 2021-03-10
  Changes: Structure summary