7Z58

Crystal structure of human Cathepsin L in complex with covalently bound Calpeptin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.130 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Calpeptin is a potent cathepsin inhibitor and drug candidate for SARS-CoV-2 infections.

Reinke, P.Y.A.de Souza, E.E.Gunther, S.Falke, S.Lieske, J.Ewert, W.Loboda, J.Herrmann, A.Rahmani Mashhour, A.Karnicar, K.Usenik, A.Lindic, N.Sekirnik, A.Botosso, V.F.Santelli, G.M.M.Kapronezai, J.de Araujo, M.V.Silva-Pereira, T.T.Filho, A.F.S.Tavares, M.S.Florez-Alvarez, L.de Oliveira, D.B.L.Durigon, E.L.Giaretta, P.R.Heinemann, M.B.Hauser, M.Seychell, B.Bohler, H.Rut, W.Drag, M.Beck, T.Cox, R.Chapman, H.N.Betzel, C.Brehm, W.Hinrichs, W.Ebert, G.Latham, S.L.Guimaraes, A.M.S.Turk, D.Wrenger, C.Meents, A.

(2023) Commun Biol 6: 1058-1058

  • DOI: https://doi.org/10.1038/s42003-023-05317-9
  • Primary Citation of Related Structures:  
    7QGW, 7QKA, 7QKB, 7QKC, 7Z3T, 7Z3U, 7Z58, 8C3D

  • PubMed Abstract: 

    Several drug screening campaigns identified Calpeptin as a drug candidate against SARS-CoV-2. Initially reported to target the viral main protease (M pro ), its moderate activity in M pro inhibition assays hints at a second target. Indeed, we show that Calpeptin is an extremely potent cysteine cathepsin inhibitor, a finding additionally supported by X-ray crystallography. Cell infection assays proved Calpeptin's efficacy against SARS-CoV-2. Treatment of SARS-CoV-2-infected Golden Syrian hamsters with sulfonated Calpeptin at a dose of 1 mg/kg body weight reduces the viral load in the trachea. Despite a higher risk of side effects, an intrinsic advantage in targeting host proteins is their mutational stability in contrast to highly mutable viral targets. Here we show that the inhibition of cathepsins, a protein family of the host organism, by calpeptin is a promising approach for the treatment of SARS-CoV-2 and potentially other viral infections.


  • Organizational Affiliation

    Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cathepsin L
A, B, C, D
220Homo sapiensMutation(s): 1 
Gene Names: CTSLCTSL1
EC: 3.4.22.15
UniProt & NIH Common Fund Data Resources
Find proteins for P07711 (Homo sapiens)
Explore P07711 
Go to UniProtKB:  P07711
PHAROS:  P07711
GTEx:  ENSG00000135047 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07711
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RN2 (Subject of Investigation/LOI)
Query on RN2

Download Ideal Coordinates CCD File 
J [auth A],
O [auth B],
T [auth C],
Z [auth D]
Calpeptin
C20 H32 N2 O4
JDNZSBPOIODDLU-ROUUACIJSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
R [auth C],
X [auth D],
Y [auth D]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
L [auth B]
M [auth B]
P [auth C]
E [auth A],
F [auth A],
L [auth B],
M [auth B],
P [auth C],
Q [auth C],
V [auth D],
W [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
K [auth B],
U [auth D]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A],
N [auth B],
S [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.130 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.18α = 105.578
b = 62.45β = 93.134
c = 67.82γ = 115.562
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Helmholtz AssociationGermanyFISCOV
Helmholtz AssociationGermanySFragX
German Federal Ministry for Education and ResearchGermany16GW0277
German Federal Ministry for Education and ResearchGermany031B0405
Slovenian Research AgencySloveniaP1-0048
Slovenian Research AgencySloveniaIO-0048

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Data collection, Database references
  • Version 1.2: 2024-02-07
    Changes: Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary