2V35

Porcine Pancreatic Elastase in complex with inhibitor JM54


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Efficiency of C-4 Substituents in Activating the Beta-Lactam Scaffold Towards Serine Proteases and Hydroxide Ion.

Mulchande, J.Martins, L.Moreira, R.Archer, M.Oliveira, T.F.Iley, J.

(2007) Org.Biomol.Chem. 5: 2617


  • PubMed Abstract: 
  • The presence of a leaving group at C-4 of monobactams is usually considered to be a requirement for mechanism-based inhibition of human leukocyte elastase by these acylating agents. We report that second-order rate constants for the alkaline hydrolys ...

    The presence of a leaving group at C-4 of monobactams is usually considered to be a requirement for mechanism-based inhibition of human leukocyte elastase by these acylating agents. We report that second-order rate constants for the alkaline hydrolysis and elastase inactivation by N-carbamoyl monobactams are independent of the pKa of the leaving group at C-4. Indeed, the effect exerted by these substituents is purely inductive: electron-withdrawing substituents at C-4 of N-carbamoyl-3,3-diethylmonobactams increase the rate of alkaline hydrolysis and elastase inactivation, with Hammett pI values of 3.4 and 2.5, respectively, which indicate the development of a negative charge in the transition-states. The difference in magnitude between these pI values is consistent with an earlier transition-state for the enzymatic reaction when compared with that for the chemical process. These results suggest that the rate-limiting step in elastase inactivation is the formation of the tetrahedral intermediate, and that beta-lactam ring-opening is not concerted with the departure of a leaving group from C-4. Monobactam sulfones emerged as potent elastase inhibitors even when the ethyl groups at C-3, required for interaction with the primary recognition site, are absent. For one such compound, a 1 : 1 enzyme-inhibitor complex involving porcine pancreatic elastase has been examined by X-ray crystallography and shown to result from serine acylation and sulfinate departure from the beta-lactam C-4.


    Related Citations: 
    • Crystallization and Preliminary Diffraction Studies of Porcine Pancreatic Elastase in Complex with a Novel Inhibitor
      Oliveira, T.F.,Mulchande, J.,Moreira, R.,Iley, J.,Archer, M.
      (2007) Protein Pept.Lett. 14: 93


    Organizational Affiliation

    i-Med-UL, Faculdade de Farmácia, Universidade de Lisboa, Av. Forças Armadas, 1600-083 Lisboa, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ELASTASE-1
A
240Sus scrofaMutation(s): 0 
Gene Names: CELA1 (ELA1)
EC: 3.4.21.36
Find proteins for P00772 (Sus scrofa)
Go to Gene View: CELA1
Go to UniProtKB:  P00772
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
J54
Query on J54

Download SDF File 
Download CCD File 
A
(2R)-3-{[(BENZYLAMINO)CARBONYL]AMINO}-2-HYDROXYPROPANOIC ACID
C11 H14 N2 O4
KGFDIRSBGRVEFZ-SECBINFHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.156 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.246α = 90.00
b = 57.938β = 90.00
c = 74.688γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOLREPphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-06-24
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance