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 9ZLX | pdb_00009zlx

Thioesterase Domain of Human Fatty Acid Synthase (FASN-TE) in apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.253 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9ZLX

This is version 1.0 of the entry. See complete history. 

Literature

Reversible, Orally Bioavailable Small-Molecule Inhibitors Occupy the Substrate Tunnel of the Thioesterase Domain of Fatty Acid Synthase.

Fromm, J., Aleshin, A., Lambert, L.J., De Backer, L.J.S., Ganji, S.R., Mattmann, M.E., Limpert, A.S., Gosalia, P., Wimer, C.D., Layng, F.I., Celeridad, M., Ardecky, R., Teriete, P., Scott, D.A., Hedrick, M.P., Smith, J.W., Sheffler, D.J., Cosford, N.D.P.

(2026) bioRxiv 

  • DOI: https://doi.org/10.64898/2026.10.01.756096
  • Primary Citation Related Structures: 
    9ZLX

  • PubMed Abstract: 

    Fatty acid synthase (FASN) is the sole enzyme capable of lipogenesis in cells and is upregulated in many cancers. Herein we report the discovery and development of SBP-5917 ( 78S ), a novel, reversible, small-molecule probe which targets the thioesterase (TE) domain of FASN. SBP-5917 and other compounds in the series possess IC 50 < 1 µM and < 5 µM for inhibiting recombinantly purified FASN-TE and cellular FASN respectively. Co-crystal structures of our inhibitors bound to the FASN-TE domain show that they are positioned in the substrate tunnel of the enzyme. Biochemical and biophysical analyses quantify the strength of compound binding and demonstrate their selectivity for FASN-TE. Preliminary pharmacokinetic studies indicate promising in vivo potency for many of the compounds in the series. SBP-5917 is the first structurally validated, reversible inhibitor of FASN-TE with demonstrated cellular target engagement and can serve as a chemical probe to investigate FASN as a therapeutic target.

Macromolecule Content 

  • Total Structure Weight: 32.52 kDa 
  • Atom Count: 2,118 
  • Modeled Residue Count: 268 
  • Deposited Residue Count: 298 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fatty acid synthase298Homo sapiensMutation(s): 0 
Gene Names: FASN
EC: 2.3.1.85 (UniProt), 2.3.1.41 (UniProt), 3.1.2.14 (UniProt), 1.3.1.39 (UniProt), 2.3.1.38 (UniProt), 4.2.1.59 (UniProt), 1.1.1.100 (UniProt), 2.3.1.39 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P49327 (Homo sapiens)
Explore P49327 
Go to UniProtKB:  P49327
PHAROS:  P49327
GTEx:  ENSG00000169710 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49327
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.253 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.949α = 90
b = 61.45β = 90
c = 76.16γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA188694

Revision History  (Full details and data files)

  • Version 1.0: 2026-11-04
    Type: Initial release