8DOY | pdb_00008doy

Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-198


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 
    0.246 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Potent and biostable inhibitors of the main protease of SARS-CoV-2.

Tsuji, K.Ishii, T.Kobayakawa, T.Higashi-Kuwata, N.Azuma, C.Nakayama, M.Onishi, T.Nakano, H.Wada, N.Hori, M.Shinohara, K.Miura, Y.Kawada, T.Hayashi, H.Hattori, S.I.Bulut, H.Das, D.Takamune, N.Kishimoto, N.Saruwatari, J.Okamura, T.Nakano, K.Misumi, S.Mitsuya, H.Tamamura, H.

(2022) iScience 25: 105365-105365

  • DOI: https://doi.org/10.1016/j.isci.2022.105365
  • Primary Citation Related Structures: 
    8DOY

  • PubMed Abstract: 

    Potent and biostable inhibitors of the main protease (M pro ) of SARS-CoV-2 were designed and synthesized based on an active hit compound 5h ( 2 ). Our strategy was based not only on the introduction of fluorine atoms into the inhibitor molecule for an increase of binding affinity for the pocket of M pro and cell membrane permeability but also on the replacement of the digestible amide bond by a surrogate structure to increase the biostability of the compounds. Compound 3 is highly potent and blocks SARS-CoV-2 infection in vitro without a viral breakthrough. The derivatives, which contain a thioamide surrogate in the P2-P1 amide bond of these compounds ( 2 and 3 ), showed remarkably preferable pharmacokinetics in mice compared with the corresponding parent compounds. These data show that compounds 3 and its biostable derivative 4 are potential drugs for treating COVID-19 and that replacement of the digestible amide bond by its thioamide surrogate structure is an effective method.


  • Organizational Affiliation
    • Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan.

Macromolecule Content 

  • Total Structure Weight: 68.64 kDa 
  • Atom Count: 4,966 
  • Modeled Residue Count: 604 
  • Deposited Residue Count: 604 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5
A, B
302Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22.69
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
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T1X
(Subject of Investigation/LOI)

Query on T1X



Download:Ideal Coordinates CCD File
G [auth A],
I [auth B]
7-fluoro-N-[(2S)-1-({(1S,2S)-1-(4-fluoro-1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
C30 H33 F2 N5 O5 S
UCQMGGDLMJSQEJ-LHXIGDLBSA-N
1PE

Query on 1PE



Download:Ideal Coordinates CCD File
C [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
MES

Query on MES



Download:Ideal Coordinates CCD File
D [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
PG0

Query on PG0



Download:Ideal Coordinates CCD File
F [auth A]2-(2-METHOXYETHOXY)ETHANOL
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free:  0.246 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.046α = 90
b = 98.942β = 106.28
c = 57.724γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
MOLREPphasing
Cootmodel building
xia2data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-24
    Type: Initial release
  • Version 1.1: 2022-11-23
    Changes: Database references
  • Version 1.2: 2022-11-30
    Changes: Database references
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-10-09
    Changes: Structure summary