8EG5 | pdb_00008eg5

huCaspase-6 in complex with inhibitor 3a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 
    0.263 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8EG5

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Engaging a Non-catalytic Cysteine Residue Drives Potent and Selective Inhibition of Caspase-6.

Van Horn, K.S.Wang, D.Medina-Cleghorn, D.Lee, P.S.Bryant, C.Altobelli, C.Jaishankar, P.Leung, K.K.Ng, R.A.Ambrose, A.J.Tang, Y.Arkin, M.R.Renslo, A.R.

(2023) J Am Chem Soc 145: 10015-10021

  • DOI: https://doi.org/10.1021/jacs.2c12240
  • Primary Citation Related Structures: 
    8EG5, 8EG6

  • PubMed Abstract: 

    Caspases are a family of cysteine-dependent proteases with important cellular functions in inflammation and apoptosis, while also implicated in human diseases. Classical chemical tools to study caspase functions lack selectivity for specific caspase family members due to highly conserved active sites and catalytic machinery. To overcome this limitation, we targeted a non-catalytic cysteine residue (C264) unique to caspase-6 (C6), an enigmatic and understudied caspase isoform. Starting from disulfide ligands identified in a cysteine trapping screen, we used a structure-informed covalent ligand design to produce potent, irreversible inhibitors ( 3a ) and chemoproteomic probes ( 13- t ) of C6 that exhibit unprecedented selectivity over other caspase family members and high proteome selectivity. This approach and the new tools described will enable rigorous interrogation of the role of caspase-6 in developmental biology and in inflammatory and neurodegenerative diseases.


  • Organizational Affiliation
    • Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, San Francisco, California 94143, United States.

Macromolecule Content 

  • Total Structure Weight: 121.23 kDa 
  • Atom Count: 8,782 
  • Modeled Residue Count: 970 
  • Deposited Residue Count: 1,036 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Caspase-6 subunit p18
A, C, E, G
150Homo sapiensMutation(s): 0 
Gene Names: CASP6MCH2
EC: 3.4.22.59
UniProt & NIH Common Fund Data Resources
Find proteins for P55212 (Homo sapiens)
Explore P55212 
Go to UniProtKB:  P55212
PHAROS:  P55212
GTEx:  ENSG00000138794 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55212
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Caspase-6 subunit p11
B, D, F, H
109Homo sapiensMutation(s): 0 
Gene Names: CASP6MCH2
EC: 3.4.22.59
UniProt & NIH Common Fund Data Resources
Find proteins for P55212 (Homo sapiens)
Explore P55212 
Go to UniProtKB:  P55212
PHAROS:  P55212
GTEx:  ENSG00000138794 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55212
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UCI
(Subject of Investigation/LOI)

Query on UCI



Download:Ideal Coordinates CCD File
I [auth B],
J [auth D],
L [auth F],
N [auth H]
(3R,5S)-1-(ethanesulfonyl)-5-phenyl-N-[4-(trifluoromethoxy)phenyl]piperidine-3-carboxamide (bound form)
C21 H23 F3 N2 O4 S
BGPUEQUEKKTRNM-IAGOWNOFSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
K [auth D],
M [auth F],
O [auth H]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free:  0.263 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.77α = 90
b = 60.88β = 91.41
c = 101.26γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
CHDI FoundationUnited StatesA-1260
Other privateAlzheimer's Association DVT-14-322219

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release
  • Version 1.1: 2023-05-24
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary