5KRE

Covalent inhibitor of LYPLAL1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 

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
  • Primary Citation of Related Structures:  
    5KRE

  • 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. We describe the discovery of potent and selective covalent small-molecule inhibitors of LYPLAL1 and their use to investigate its role in hepatic metabolism ...

    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

    Worldwide Medicinal Chemistry and §Pharmacokinetics, Dynamics, & Metabolism, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysophospholipase-like protein 1A239Homo sapiensMutation(s): 1 
Gene Names: LYPLAL1
EC: 3.1.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q5VWZ2 (Homo sapiens)
Explore Q5VWZ2 
Go to UniProtKB:  Q5VWZ2
PHAROS:  Q5VWZ2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6WG
Query on 6WG

Download Ideal Coordinates CCD File 
B [auth A](2~{R})-2-phenylpiperidine-1-carbaldehyde
C12 H15 N O
MUZIXORETQNNBG-GFCCVEGCSA-N
 Ligand Interaction
NO3
Query on NO3

Download Ideal Coordinates CCD File 
C [auth A]NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.41α = 90
b = 61.44β = 90
c = 75.98γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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