5KRE | pdb_00005kre

Covalent inhibitor of LYPLAL1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.212 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.165 (Depositor) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/acschembio.6b00266
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 26.77 kDa 
  • Atom Count: 1,942 
  • Modeled Residue Count: 224 
  • Deposited Residue Count: 239 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lysophospholipase-like protein 1239Homo sapiensMutation(s): 1 
Gene Names: LYPLAL1
EC: 3.1.2 (PDB Primary Data), 3.1.2.22 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q5VWZ2 (Homo sapiens)
Explore Q5VWZ2 
Go to UniProtKB:  Q5VWZ2
PHAROS:  Q5VWZ2
GTEx:  ENSG00000143353 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5VWZ2
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.212 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.165 (Depositor) 
  • R-Value Observed: 0.168 (Depositor) 
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

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • 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
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary