5KRE

Covalent inhibitor of LYPLAL1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of a Selective Covalent Inhibitor of Lysophospholipase-like 1 (LYPLAL1) as a Tool to Evaluate the Role of this Serine Hydrolase in Metabolism.

Ahn, K.Boehm, M.Brown, M.F.Calloway, J.Che, Y.Chen, J.Fennell, K.F.Geoghegan, K.F.Gilbert, A.M.Gutierrez, J.A.Kalgutkar, A.S.Lanba, A.Limberakis, C.Magee, T.V.O'Doherty, I.Oliver, R.Pabst, B.Pandit, J.Parris, K.Pfefferkorn, J.A.Rolph, T.P.Patel, R.Schuff, B.Shanmugasundaram, V.Starr, J.T.Varghese, A.H.Vera, N.B.Vernochet, C.Yan, J.

(2016) Acs Chem.Biol. 11: 2529-2540

  • DOI: 10.1021/acschembio.6b00266

  • PubMed Abstract: 
  • Lysophospholipase-like 1 (LYPLAL1) is an uncharacterized metabolic serine hydrolase. Human genome-wide association studies link variants of the gene encoding this enzyme to fat distribution, waist-to-hip ratio, and nonalcoholic fatty liver disease. W ...

    Lysophospholipase-like 1 (LYPLAL1) is an uncharacterized metabolic serine hydrolase. Human genome-wide association studies link variants of the gene encoding this enzyme to fat distribution, waist-to-hip ratio, and nonalcoholic fatty liver disease. We describe the discovery of potent and selective covalent small-molecule inhibitors of LYPLAL1 and their use to investigate its role in hepatic metabolism. In hepatocytes, selective inhibition of LYPLAL1 increased glucose production supporting the inference that LYPLAL1 is a significant actor in hepatic metabolism. The results provide an example of how a selective chemical tool can contribute to evaluating a hypothetical target for therapeutic intervention, even in the absence of complete biochemical characterization.


    Organizational Affiliation

    Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Research Unit, Pfizer Inc. , 610 Main Street, Cambridge, Massachusetts 02139, United States.,Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysophospholipase-like protein 1
A
239Homo sapiensMutation(s): 0 
Gene Names: LYPLAL1
EC: 3.1.2.-
Find proteins for Q5VWZ2 (Homo sapiens)
Go to Gene View: LYPLAL1
Go to UniProtKB:  Q5VWZ2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NO3
Query on NO3

Download SDF File 
Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
6WG
Query on 6WG

Download SDF File 
Download CCD File 
A
(2~{R})-2-phenylpiperidine-1-carbaldehyde
C12 H15 N O
MUZIXORETQNNBG-GFCCVEGCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.410α = 90.00
b = 61.440β = 90.00
c = 75.980γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
BUSTER-TNTrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-07-07 
  • Released Date: 2016-07-20 
  • Deposition Author(s): Pandit, J.

Revision History 

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-09-28
    Type: Database references