6QBU

Crystal structure of Porcine Pancreatic Elastase (PPE) in complex with the 3-Oxo-beta-Sultam inhibitor LMC188


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.135 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

3-Oxo-beta-sultam as a Sulfonylating Chemotype for Inhibition of Serine Hydrolases and Activity-Based Protein Profiling.

Carvalho, L.A.R.Almeida, V.T.Brito, J.A.Lum, K.M.Oliveira, T.F.Guedes, R.C.Goncalves, L.M.Lucas, S.D.Cravatt, B.F.Archer, M.Moreira, R.

(2020) ACS Chem Biol 15: 878-883

  • DOI: https://doi.org/10.1021/acschembio.0c00090
  • Primary Citation of Related Structures:  
    6QBU, 6QEN, 6QEO, 6SMA

  • PubMed Abstract: 

    3-Oxo-β-sultams are four-membered ring ambident electrophiles that can react with nucleophiles either at the carbonyl carbon or at the sulfonyl sulfur atoms, and that have been reported to inhibit serine hydrolases via acylation of the active-site serine residue. We have developed a panel of 3-oxo-β-sultam inhibitors and show, through crystallographic data, that they are regioselective sulfonylating electrophiles, covalently binding to the catalytic serine of human and porcine elastases through the sulfur atom. Application of 3-oxo-β-sultam-derived activity-based probes in a human proteome revealed their potential to label disease-related serine hydrolases and proteasome subunits. Activity-based protein profiling applications of 3-oxo-β-sultams should open up new opportunities to investigate these classes of enzymes in complex proteomes and expand the toolbox of available sulfur-based covalent protein modifiers in chemical biology.


  • Organizational Affiliation

    Department of Medicinal Chemistry, Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmacia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chymotrypsin-like elastase family member 1240Sus scrofaMutation(s): 0 
EC: 3.4.21.36
UniProt
Find proteins for P00772 (Sus scrofa)
Explore P00772 
Go to UniProtKB:  P00772
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00772
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HVZ
Query on HVZ

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[[1-[(4-chlorophenyl)methyl]-1,2,3-triazol-4-yl]methyl]-2-hydrosulfonyl-2-methyl-propanamide
C14 H17 Cl N4 O3 S
WWIJWVXKLYGOJA-UHFFFAOYSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
E [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.135 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.548α = 90
b = 57.551β = 90
c = 74.594γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
BUSTER-TNTrefinement
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fundacao para a Ciencia e a Tecnologia (FCT)PortugalSAICTPAC/0019/2015
Fundacao para a Ciencia e a Tecnologia (FCT)PortugalPTDC/BBB-BEP/2463/2014
Fundacao para a Ciencia e a Tecnologia (FCT)PortugalPEst-OE/SAU/UI4013/2014
Fundacao para a Ciencia e a Tecnologia (FCT)PortugalSFRH/BD/100400/2014
Fundacao para a Ciencia e a Tecnologia (FCT)PortugalIF/00472/2014

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-08
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary