6QEN | pdb_00006qen

Crystal structure of Porcine Pancreatic Elastase (PPE) in complex with the 3-Oxo-beta-Sultam inhibitor LMC240


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.174 (Depositor), 0.181 (DCC) 
  • R-Value Work: 
    0.142 (Depositor), 0.154 (DCC) 
  • R-Value Observed: 
    0.143 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6QEN

Ligand Structure Quality Assessment 


This is version 1.4 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 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.

Macromolecule Content 

  • Total Structure Weight: 26.68 kDa 
  • Atom Count: 2,091 
  • Modeled Residue Count: 240 
  • Deposited Residue Count: 240 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
J05

Query on J05



Download:Ideal Coordinates CCD File
B [auth A]1-[[1-[(4-bromophenyl)methyl]-1,2,3-triazol-4-yl]methylamino]-2-methyl-1-oxidanylidene-propane-2-sulfonic acid
C14 H17 Br N4 O4 S
MXYSCNLKJAGAQI-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: 1.20 Å
  • R-Value Free:  0.174 (Depositor), 0.181 (DCC) 
  • R-Value Work:  0.142 (Depositor), 0.154 (DCC) 
  • R-Value Observed: 0.143 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.127α = 90
b = 57.71β = 90
c = 74.646γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Portugal--

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Database references
  • Version 1.2: 2020-04-29
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary