7TVS

The Crystal Structure of SARS-CoV-2 Omicron Mpro (P132H) in complex with demethylated analog of masitinib

• PDB DOI: https://doi.org/10.2210/pdb7TVS/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Severe acute respiratory syndrome coronavirus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-02-05 Released: 2022-02-16 
• Deposition Author(s): Tan, K., Maltseva, N.I., Endres, M.J., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.225 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Starting Model: experimental

Literature

The Crystal Structure of SARS-CoV-2 Omicron Mpro (P132H) in complex with demethylated analog of masitinib

Tan, K., Maltseva, N.I., Endres, M.J., Joachimiak, A.

To be published.

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)

Macromolecule Content

• Total Structure Weight: 34.51 kDa 
• Atom Count: 2,411 
• Modelled 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 nsp5	A	306	Severe acute respiratory syndrome coronavirus	Mutation(s): 1  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XNJ (Subject of Investigation/LOI)	B [auth A]	N-(4-methyl-3-{[4-(pyridin-3-yl)-1,3-thiazol-2-yl]amino}phenyl)-4-[(piperazin-1-yl)methyl]benzamide C27 H28 N6 O S LBWSNUMFQJZFGI-UHFFFAOYSA-N
DMS	C [auth A], D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.225 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.08	α = 90
b = 80.888	β = 114.329
c = 51.912	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-16 
Deposition Author(s): Tan, K., Maltseva, N.I., Endres, M.J., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201 700060C

Revision History  

• Version 1.0: 2022-02-16
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description