5SYM

Cocrystal structure of the human acyl protein thioesterase 1 with an isoform-selective inhibitor, ML348


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Molecular Mechanism for Isoform-Selective Inhibition of Acyl Protein Thioesterases 1 and 2 (APT1 and APT2).

Won, S.J.Davda, D.Labby, K.J.Hwang, S.Y.Pricer, R.Majmudar, J.D.Armacost, K.A.Rodriguez, L.A.Rodriguez, C.L.Chong, F.S.Torossian, K.A.Palakurthi, J.Hur, E.S.Meagher, J.L.Brooks, C.L.Stuckey, J.A.Martin, B.R.

(2016) ACS Chem Biol 11: 3374-3382

  • DOI: 10.1021/acschembio.6b00720
  • Primary Citation of Related Structures:  
    5SYM, 5SYN

  • PubMed Abstract: 
  • Post-translational S-palmitoylation directs the trafficking and membrane localization of hundreds of cellular proteins, often involving a coordinated palmitoylation cycle that requires both protein acyl transferases (PATs) and acyl protein thioesterases (APTs) to actively redistribute S-palmitoylated proteins toward different cellular membrane compartments ...

    Post-translational S-palmitoylation directs the trafficking and membrane localization of hundreds of cellular proteins, often involving a coordinated palmitoylation cycle that requires both protein acyl transferases (PATs) and acyl protein thioesterases (APTs) to actively redistribute S-palmitoylated proteins toward different cellular membrane compartments. This process is necessary for the trafficking and oncogenic signaling of S-palmitoylated Ras isoforms, and potentially many peripheral membrane proteins. The depalmitoylating enzymes APT1 and APT2 are separately conserved in all vertebrates, suggesting unique functional roles for each enzyme. The recent discovery of the APT isoform-selective inhibitors ML348 and ML349 has opened new possibilities to probe the function of each enzyme, yet it remains unclear how each inhibitor achieves orthogonal inhibition. Herein, we report the high-resolution structure of human APT2 in complex with ML349 (1.64 Å), as well as the complementary structure of human APT1 bound to ML348 (1.55 Å). Although the overall peptide backbone structures are nearly identical, each inhibitor adopts a distinct conformation within each active site. In APT1, the trifluoromethyl group of ML348 is positioned above the catalytic triad, but in APT2, the sulfonyl group of ML349 forms hydrogen bonds with active site resident waters to indirectly engage the catalytic triad and oxyanion hole. Reciprocal mutagenesis and activity profiling revealed several differing residues surrounding the active site that serve as critical gatekeepers for isoform accessibility and dynamics. Structural and biochemical analysis suggests the inhibitors occupy a putative acyl-binding region, establishing the mechanism for isoform-specific inhibition, hydrolysis of acyl substrates, and structural orthogonality important for future probe development.


    Organizational Affiliation

    Program in Chemical Biology, ‡Department of Chemistry, §Department of Biophysics, and ∥Life Sciences Institute, University of Michigan , 930 N. University Ave., Ann Arbor, Michigan 48109, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl-protein thioesterase 1A, B230Homo sapiensMutation(s): 0 
Gene Names: LYPLA1APT1LPL1
EC: 3.1.2
UniProt & NIH Common Fund Data Resources
Find proteins for O75608 (Homo sapiens)
Explore O75608 
Go to UniProtKB:  O75608
PHAROS:  O75608
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
71Q (Subject of Investigation/LOI)
Query on 71Q

Download Ideal Coordinates CCD File 
C [auth A], M [auth B]N-[2-chloro-5-(trifluoromethyl)phenyl]-2-[4-(furan-2-carbonyl)piperazin-1-yl]acetamide
C18 H17 Cl F3 N3 O3
OXKNHBBDOIMFFQ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], L [auth A], N [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], K [auth A], O [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
71Q BindingDB:  5SYM Ki: min: 280, max: 1.00e+4 (nM) from 8 assay(s)
Binding MOAD:  5SYM Ki: 280 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.67α = 90
b = 73.69β = 90
c = 81.82γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
MOLREPphasing
SCALAdata scaling
MOSFLMdata reduction
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR00 CA151460
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesDP2 GM114848

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-11-09
    Changes: Database references
  • Version 1.2: 2016-12-28
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence